Before anyone says SEARCH, let me preface that I have been doing nothing but researching this very issue for hours upon hours. I must have over 30 hours of searching and reading posts on this site and I am still no further along than I was when I started.
I have developed the following conclusions based on all my reading:
1) A stock L28ET provides the most bang for the buck - that is until you decided to increase the horsepower beyond stock.
2) Building a 3.0 or 3.1L N/A stroker is relatively pricey and the gains, while impressive, are limited. Once you build it out, there is not too much more you can do to increase your horsepower.
Now comes my conjecture:
3) Building an L28ET to produce the same power as 3.1L stroker will cost just as much, if not slightly more, than building the stroker. I say this because, based on my reading, if you want to increase your power beyond stock in the L28ET, you are looking at an aftermarket fuel management software (MS), larger injectors, larger turbo, intercooler, larger fuel pump/FPR, boost controller, etc. The most significant cost is the software.
Ok, after saying all of this, and having a defined goal in mine of producing 200 to 220 RWHP, both options are in the running but the stroker is slightly in the lead.
I like turbo charged engines, especially on race gas and a cold day (thanks to my 2002 S4). However, I also like have gobs of torque on hand at low RPMs. Waiting for the turbo to spool up and hit peak book is aggravating.
I keep flip-flopping back and forth. I was originally set on a stroker, but then the L28ET swap kept nagging at me due to its initial low cost. However, upon further reflection (see #3), this cost difference evaporates once you try to achieve similar HP numbers (unless I am mistaken). Saying that, the sky is the limit once you get MS as far as power is concerned with the L28, so why limit yourself to 200/220.
This is a street car and will be driven quite frequently (not a daily driver, but I will take it into work occassionally).
Your sage advice is most certainly welcome.