One of the things I can't understand is when a state takes a unilateral decision regarding affairs in your country, you can't do anything about it. I have played Prussia till '59 and grew increasingly pissed at the Austrian army lounging in Berlin because it was at war with Britain... go figure. So I broke off my alliance with Austria in order to kick them out. 2 turns later and Austria just unilaterally decided that it had the right to walk in Prussia and I couldn't do anything about it. Frankly I'm lost on this one...
Secondly, the alliance system at the begining of the game tends to destabilise the game. The alliance between Prussia and Austria and the one between Austria and Russia has far reaching effects. Usually Sardinia gets overrun by Austrian forces when the Crimean War breaks out. France is essentially on the defensive and the UK is nowhere to be found. (Incidentally when Austria wakes up it seems to go on a conquering spree of the minor states that surround it) Since France doesn't seem to be allied with either the UK or S-P, this leads to imbalances. Frankly I believe that the three states should be neutral towards each other, though with high recognition of each other that gets eroded over time. That would allow each major power to play its own game. (I haven't got there yet but I believe that come the time for German Unification, Russia would barge in on Prussia)
Regarding Germany, maybe it would be better if both Prussia and Austria are allied to the minor states, so that if one of them decides to act funny, the other will act as a counterweight.
The same should apply to the minor states in Italy, the bulk of which were Austrian satellites. If they are allied to the Austrians, it should prevent them from falling prey to the Austrians. Austria was all about preserving the balance of power and thus supported all the small states.
Don't take it as a rant but I'm just putting my ideas forward on these issues....