Tried 'em both
Started the summer with the Fi2000, which I ordered after putting the cobra swepts on the bike and it ran like crap; very cold-startish, easy to stall at lights, somewhat erratic at different points in the powerband. Got the 2000 and the instructions say start with factory default of 1-2-0; except mine was factory default of 0-0-0, so I put it on like that and guess what THE BIKE RAN GREAT ... go figure. Ran it like that till I added the S&S air intake and bike ran crappy again. The FI got it running better, but I never did find a dial adjustment that satisifed me. And I tried DOZENS of settings. The best adjustment I got was to max out the settings near the high end of each pot, which ran better but I was often smelling fuel at lights, so at end of summer I said hell with it and got the PC5.
Only had the pc5 on there for a short while before the snow fell so I can only offer the following: using S&S dyno'ed map for fury/s&s intake/cobra swepts with baffles, the bike ran pretty smooth thru the powerband, but wasn't quite as strong off the line as the fi2000 made it, which was something I really liked. This is adjustable I'm sure, with nothing more than a laptop and some guys from NASA to come over to your house to help out. meh ...
CONCLUSION: [for what it's worth] FI2000: flimsy, not particularly well-built, and settings seem to produce wildly different results even for guys with same bike and intake/exhaust setup. HOWEVER, and this is a big however: the unit does work and you CAN do it yourself, which is worth a lot. Yeah, it may be kinda half-assed, bootstrap procedure, but at least you can do it and I think eventually, you make enough settings alterations, odds alone will dictate you'll get it right even if by accident. (If I were doing it over, I think I'd give the Fi2000 another couple weeks to see if I'd get it just right, but I wanted the pc5 and didn't realize at that time what the pc5 map situation really involved.)
PC5 - *much* better built, higher quality control, and allows for much finer tuning HOWEVER (same big however) if you don't have access to a skillfully operated dynotune machine, and the cash for a dyno run (as much as the pc5 itself in some cases), or a map made by someone who DID have access to the above, yer screwed. The company offers a base map, based on stock configuration, personally I don't think it'll do a damn thing for new pipes/air intake. S&S offers free maps for several configurations, albeit all with their air cleaner, which is reasonable enough. upshot is, yer not gonna do any casual adjustments with a pc5 - have the means and time to get it set right, whatever it takes, or you might be happier with the 2000. Also, signifigant changes in the future could mean a repeat of the whole dyno/map thing.
If you're leaning towards the PC5, don't take it for granted you can get it dyno'ed even if you decide to spend the money - call around first and find out who will do it, when they can get you in and how much they want - there are places you can't even get it done. In a couple years there'll be more customer-generated maps out there I'm sure, but for now it can be a serious pain in the ass. The Fi2000 will spare you all the map crap, but you might spend a lot of time trying to 'bootstrap' the settings to where they need to be.
I guess the only thing I can see with absolute certainty on this issue is I'm starting to really HATE FUCKING FUEL INJECTION; GIMME BACK MY CARBS!!!