Boy Twisty you ask the simple questions don't you? There are so many chickens and eggs in that little doosy that you could start a poultry farm and omelette restaurant and still have both chickens and eggs left over.
i can understand why bigger bore means more power (thru more gas/air capacity)
I assume you mean increased capacity [not just bigger bore] is an obvious path to more power.
why isn't it best to have as wide a bore as possible and a short a stroke as possible?
Modern, high revving racing engines do just that. But there is a limit on how quickly you can get enough mixture into the cylinder when you have an extremely short stroke [with resultant high revs]. Not to mention the problems of incomplete combustion due to the high flame speed required.
In a modern F1 engine, revving to 18,000 rpm - the cylinder has to be filled and emptied 150 times per second. At this speed the pistons are experiencing acceleration loads of up to 8500g. The conrod stretches by about .33 of a mm whilst slowing down the piston. The piston is experiencing loads including combustion approaching 6 tonnes. The valves have a mass of only 50g but because they are opening and closing 150 times a second they are experiencing 10,000g and have an 'apparent' weight of 500kg each. Add in the extreme temperatures and you have a living hell that somehow survives for 1500 klms. Amazing stuff.
I would suggest you get hold of some of Kevin Camerons [tech editor at Cycle World] writings to get a better understanding of your question. It is fascinating to put together little pieces of the puzzle in your mind - and just when you think you are getting somewhere, some new development comes along and makes the impossible, possible.
Good luck
VMX42
P.S. and be careful you don't get your 'jugs' mixed up. That could be painful.