Transport capacity.
Do you accomplish this by editing the statistics in the game files for naval units? Anyway, I don't know if this is logical. Ships of the line (i.e. warships) could in fact carry a great many troops, and did in many occasions.
While it's true that warships sometimes carried troops, they did not, as a rule, carry 1000 armed ground troops or 1000 armed cavalry plus mounts or even 10 fully-equipped pieces of field artillery -- not to mention the seige trains and miscellaneous stores, equipment and baggage that invariably followed a land army. I prefer the rule to reflect the rule rather than the exception. The naval logistical arm for ground troops, throughout history, has been the transport, not the warship. For example, of the 130 ships in the Spanish Armada, only about 70 were considered warships (and many of those were merely armed merchantmen). And the invasion failed, in part, because the Duke of Parma, in Flanders, had nothing but transports and wasn't convinced that the Armada could adequately defend them. EU2 currently simulates virtually none of this; I doubt anyone ever builds more than a handful of Transports in the game. My house rule attempts to make the Transport a real necessity instead of just a little-used curiousity. And to require some planning and expense to become a true naval power.
As for implementation, I just use will power -- I don't move it unless I have enough Transports to move it. Imperfect, but it works.
Recruitment of armies.
Olafs idea about not recruiting from conquered provinces make sense, but I'd rather say wait a few years. Perhaps untill nati. is at 2 %. In WW2 for instance, Germany recruitted quite a lot of anes to Waffen SS, and even more to other corps. That just goes to show that there will always be someone willing to join the invaders army... and even more in this time, when nationalism were not as common.
True, but the bulk of the seasoned armies of most nations throughout this period consisted of either homeland troops or mercenaries. This is especially so for top-quality units. (I think your examples prove that.) For example, a source I have says that England sent about 90,000 troops to France between 1415 and 1450 and describes the contribution of Normandy and other mainland provinces as "negligible." EU2 doesn't distinguish between the quality of troops recruited at home and those recruited in some distant province that you just conquered, and that seems highly unrealistic to me. The rule I actually use (I was in a hurry before) is that I recruit Cavalry and Artillery only from core provinces. Any reinforcements from other provinces can be infantry only, and I limit myself to mercenary infantry (I disband the cavalry/artillery components) from foreign provinces until they have a governor. This maintains the qualitative advantage of using homeland troops.
Together, the two rules greatly enhance the game, I think. For example, I just started a 1419 GC as England and found that it was virtually impossible to hold Gascony against a concerted assault from France and her allies if I couldn't build troops at will in Gascony. And since I had only six transports, I had limited ability to ship troops from England -- and could do so only at the cost of having my transports unavailable to ship reinforcements to Henry V. Far from being the usual cakewalk, I actually had to work and plan to hold on to Gascony while still supporting the main thrust with Henry V. Much more realistic and fun.