I've got 6 or 8 A2s in various stages of repair, ranging from turn-key to work dump to parts vehicles, and I've had some really pretty low-mile A2s in the past. I've played with, praised, worked and cursed these vehicles. I've also got several 5.9 Cummins around here, all the stuff to put one in a Deuce (bellhousing, flywheel, compressor, etc) even an Allison 545.
But I paid $9,245.32 total for an M35A3 w/w with 1600 miles on it and haven't regretted it a bit. There's just no comparison between an A2 and A3 EXCEPT the A2 is cheaper and probably tougher, at least you aren't as uptight about beating on a $2000 truck! The A3 auto is proven, works great and is common as dirt (yes, look under a schoolbus) , the CAT 3116 is lightyears ahead of our friend ol' multi, that bearing spinning beast. Air-o-Matic steering and the auto makes it a pleasure to drive in parades, around town and riding trails, women can actually drive the thing. CTIS is handy when you're alternatively on trails and pavement. This A3 even SMELLS different, maybe it's all the rubber on the floor, sound-deadner or undercoat...
Is it better? To me, yes, without a doubt. Isn't it expensive? No, not when you think about building an A2 to the same point: $1200 non runner A2, $4000 LOW mile 5.9 or 3116, $1200 Air-O-Matic, $1000 of coversion bits (b-housing, flex-plate, starter, hoses, intercooler, etc. think about it), $1800 re-con Allison 545... You'll have better than $8G and countless hours of work (or a fortune in someone else's work) in your A2 and still not have CTIS, the nice driver's seat, a real heater, sound-deadning and all the benefits of a really low mile vehicle like few to no driveline leaks, perfect tires, unrusty windshields and no general 'crustiness' of old M35s.
If you like the features and can swing the dough, save yourself a bunch of time, aggravation and money and buy an A3 while you still can...