The 05-06 are a tougher sled all around, a-arms, rear tunnel sections, a little heavier but alot stronger. IMHO, better boards or similar, 08+ spindles, diff skis, and the new 09 front end will make a ton of difference. If you are starting with a 600 base you have alot of options for powerplants. 600HO Carb/CFI, 600 IQR, 660 Carb/CFI, 685 Carb, 700 CFI, 770 CFI, 800CFI/800BB Carb, 800 Carb(600 IQR base), 840 CFI(700 Base), 860 Carb(600 HO base), 860 CFI, 910/950 BB(800 BB Base), single pipe/twin pipe/turbo it all fits, the small blocks are a bolt in opperation (basically), BB will need a motor plate and pipe(s) fitted.
755/866 base is also a solid starting point, the 755 can be fairly easily upgraded to 866,
theres a 975kit(carl's) for the 866, 1140 if you have deep pockets. These motors respond well to mods and when well set up are good options and can be done cheaply and the entry cost is well below that of even an 07 600, they can be found new for sub $6000.
The other option is the FST, these are incredible when modded but have issues that can't be moddded out of them, but if a guys on his toes with maintenance and is willing to follow the path less travelled theres an underground following with some awesome gains with simple ECU tuning and some watercraft (same engine) parts.