Go with what you like. There is some debate on the ease of maintenance. I don't find my ST4 bad at all. Given my ST versus any other ST, I would keep mine solely because I have it where I like it and I know it so well. Of course, there is a never ending list of mods / maint that I'd like to accomplish someday.
IMHO, the only trick is learning how to remove the side panels without messing with the upper fairing. It is a different trick on the first gen models. That is the largest time saver on maintenance. Everything else is based on knowing the bike and that it is simply a great, yet under-appreciated, Ducati.
That said, if something unforeseen happened to mine, I would be simply looking for the best deal on another ST: price/mods versus age/mileage/condition.
As to which model to buy, as tonered says I would be looking for one with the best mods already in place regardless of model although being the ST4s mark I or II would be a good starter for me but I am biased and never ridden the st3. Maintenance on either would be similar and not worth bringing into the equation.
I will weigh in here...
I owned a 2005 ST3 with Cogent DYnamics suspension set up.
It was an AWESOME machine..
LeoVince slipons made music...
I now have an ST4S and the engine is much more powerful according to the perfectly accurate and calibrated BUTT DYNO!!
Suspension is also quite inspiring...
But the engine is magic..
Go with the ST4S if you can...Go with the ST3 if it has some good upgrades...like fork work and shock work done by Cogent Dynamics..
Also...keep a few thou in reserve to purchase the upgrades that make the bike YOURS!!!