1. There are 7 core slots in v1.8 in the early scenarios. In previous versions there were more but I decided to reduce it so that players can start the big scenario with a more equal chance (i.e. less variation in the core army).
2. Sparatacus' 1941 scenario is similar to BE in many ways. Actually it was one of the main inspirations for me to make a grand scenario. First its map is smaller, about half the size. Also that one only uses vanilla units from the base game and there are no additional modded units if I remember well. "1941" has less historical events and scripts. However, that one is well suited for multiplayer, while I just have not have the time to make BE multiplayer compatible. Some players tried BE in multi, but it is way too unbalanced as the Allied (AI) side has much more resources, just as historically. Historically the Allies produced four times more aircraft and tanks and had a lot more soldiers and oil and money and everything than the Axis and it is well reflected in my mod. In "1941" the the two sides are more balanced which better suits multiplayer game.
Apart from BNC's grand scenarios there is Akkula's Soviet Storm mod, which includes a grand Great Patriotic War, playable from the Soviet side.
Another similar Soviet grand strategy mod is currently under development by Intenso82.
3. It had to be bad luck. Very bad luck. If you try again, I am pretty sure you will get better results. But, despite popular belief, Polish Air Force was not that bad in WW2 as they are often depicted in games. They were well trained and highly motivated. Despite flying outdated planes and being outnumbered, they managed to achieve a nearly 1 to 1 kill to loss ratio against the Luftwaffe.
4. Historically the Italian Navy (Regia Marina) did not really shine in WW2 against the Royal Navy. There were many reasons, e.g. Italian warships had no radar for a long time, and even then their radars were inferior to the British ones. For example on one occasion British destroyers managed to sink two Italian cruisers with torpedoes at night using their radars and attacking with the land behind their back.
https://en.wikipedia.org/wiki/Battle_of_Cape_Bon_(1941)
Also, the British had better training, better morale, better intelligence (they could read coded Italian messages while the Italians could not), and in general their ships were better protected (most Italian cruisers sacrificed armour for more speed).
These are all reflected in the different stats and the lower experience of the Italian ships.
I do not want to put more but weaker Allied ships on the map as the current numbers reflect historical numbers and ratios.
Historically the Italian Navy was pretty much obliterated by 1943, losing most of its destroyers, cruisers and submarines. Only the battleships survived intact, but there was no fuel for them.
To maximize the effectiveness of the Italian navy in this mod you should attack British destroyers with Italian capital ships from a distance, then first weaken enemy battleships and cruisers with Axis submarines and bombers. It is important to weaken the Allied ships first as the AI is not smart enough to move its ships to ports for repair. Weakened British ships are then much more vulnerable to the Italian surface ships.
Against enemy submarines tactical bombers are the best. Again, once they are weakened either by bombers or destroyers, they are easier to destroy. And as the AI would not repair them, players can afford losing more destroyers to weaken enemy submarines and then repair the destroyers in home ports.
Even then there will be heavy losses and there is a good chance that the Italian navy will be mostly sunk by 1943, just as historically. But if they can effectively support landings and land operations by then it does not really matter.
Malta should be bombed to submission by tactical bombers. The Ju 87 Stuka with the hero Rudel is the best unit to do so. You just need to transfer it to the Med and provide enough fighter protection. That will do the trick. Historically, the Luftwaffe never took the bombing of Malta seriously enough. They always transfered their bombers to another front just as Malta was on the verge of collapse and left it to the Italians to finish the job but they were unable to do so.
5. Yes, each Würzburg should give +1 ini to any Axis fighter within its range of 3 hexes. More radars can give more ini bonus. You can check it with the battle predicion with the Ctr+left click.
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6. It cannot be avoided by scripting as rain comes random and is not connected with the scripts. But you only get it in rain, not during the winter months when it is snowing. It should not happen too often, unless you are very unlucky or do not keep the number of enemy bombers low all the time. One could say that those bombers should be destroyed in good weather before the rain comes.
7. If the Soviets loss the Caucasus they will get less reinforcements after a while. It does not affect the Western Allies as they have their own oil fields in the Middle East and in the US.
the rest:
1. Small calibre AA much, much stronger against soft targets: I also find them a bit weak, but would not make them much stronger as their primary goal should be to destroy enemy aircraft. If I give them way too high soft attack players would mainly use these against ground targets which would not be historically accurate as it was only their secondary role. So one has to be careful here, but I can imagine a little increase.
2. Dora gun: there were too few of these to be included in this mod as a seperate unit. Remember that one artillery unit represents about 1.000 artillery guns in the mod. The current Karl-Gerat unit symbolises all the very heavy artillery that the Germans had, including the Dora guns.
3. Initiative in ambushes: I cannot modify game mechanics. It is all hard coded and cannot be modded without hacking the game.
4. More Croatian units: normally in the mod one infantry unit represents 2-3 infantry divisions or an army corps with 30.000-40.000 men. Even then there are some exceptions, for example the Spanish Blue Divison represents a single divison with 20.000 men. As far as I know the Croat legions were less numerous, the Italian-Croat Legion was two-battalion strong, subordindated to the Italian 3rd Mobile Division. The German-Croat Legion was a three-battalion infantry regiment with an artillery battalion. Even if combined these do not make up even for a single three-regiment division and that's why I did not add them. The majority of the Croat forces were used in the Balkans against the partisans. I can possibly add another Croat infantry unit though, to represent those 3 German-Croat divisons raised in 42-43 and used in the Balkans. I think most players would welcome it as the partisans are getting stronger as well from that time. Or alternatively can be sent to any frontline and used there.
Even though I understand your reasoning, I would not give Bf 110 to the Croats as they flew the Bf 109 and the Do 17 in the east. The main problem here is that the Minor Axis air forces are already somewhat over represented in the mod at the current scale. Even though they represent the whole air forces of those nations and not only those few squadrons that were actually used in the east. Basically I fear that giving even more would further distort the Minor Axis air units vs. Luftwaffe ratio. If I give Croat air unit(s), to make it fair, I should also add Slovak and Bulgarian ones. Then I would need to add more Lufwaffe units to compensate and then even more Allied air units to compensate for all the above. In the end there would be a lot more air units in the mod significantly changing the balance and playability. Italy, Hungary, Romania and Finland were the main Axis allies in Europe, who had significant numbers of tanks, aircraft, home production, etc. and a more or less independent government and at this scale I only chose them to have the full range of units in the mod.
Regarding SS/elite units: basically all those "elite" units which are added after 1941, with or without a hero, can be regarded as new SS units. Just as some good units with 200 or more experience in turn 1. However, the basic assumption of this mod is that the Führer is removed from power in 1941 (otherwise how would the player gain full control over the Axis armies?) and after that there might not be more SS units raised. I would like to leave it to the players' imagination/interpretation to decide which one applies but there will be no direct referencies to SS or other Nazi formations in this mod.
Obviously there were many other special units in WW2 but it is not possible to add them all at this scale. Not even most of them. I did add some like Brandenburgers or British commandoes but at this scale it is simply not possible to add many more as the map would be full of units and there would be no room to maneuver.
As far as I know Hiwis were mainly used in support role and only rarely used in the frontline. In most cases they were subordinated to standard Wehrmacht divisions. As such they supposed to be part of the reinforcements given to German units after 1942/43. Some historical units recruited from the occupied parts of the USSR such as the Kosaken cavalry or the Latvian Legion does appear, though.
I am just taking a little break from modding PzC, as I think v1.8 is fairly good at the moment. At least I do not seem to get many complaints for bugs and stuff. "If it aint broken, dont fix it!" I did make a few changes though, mainly graphical ones, but these do not justify a new update. But I intend to make a new release at some point in the future. 
Autumn 43 the Panthers are coming. That will make it easier against the "endless" number of Red Army tanks.