We have both - and, as has been said, they are different animals that look the same.
I love driving both - the 2.0 for the sheer chuckability and the 3.0 for the acceleration which still puts a grin on my face when I floor it.
The TS engine is, imo, a great piece of kit and fantastic at high revs. 95% of the time you don't need the extra acceleration so don't miss a V6. The Busso V6 engine is fantastic and well worth having for that 5% of the time.
If you get a sorted V6 it will be just as reliable as anything else IF you service it on time and replace stuff as it wears. I use mine as a daily driver. The 2.0 is now LizR's car which she too uses daily and it is near enough up to 170k miles and going strong.
I agree the 2.0 is probably not really worth tuning (unless you do such things for fun) as you can pick up a V6 for the price it would cost to do for a decent material gain.
If I had to choose? I had the 2.0 for 7 years before Liz took it on and it was the best, most enjoyable car I had ever had. I am glad I can still get to drive it on occasion. I have only had the V6 for 5 months (I've put 9k mostly pleasure miles on it since then
). It took me about two months to adjust to the roadholding over the 2.0 - even more noticeable as it's a Spider - and had a couple of hairy moments. Having learned it's limits I feel as confident in it around the twistys as I do in the 2.0 although I concede the 2.0 has the edge there. My choice, however would be the V6 - I would truly miss the power.