I've put on 3000k's on my bike now, with quite an extensive list of mods, but no REAL show stoppers.
The throttle issue is pretty common on all bikes IMHO, yes even the FZ/MT-07 had that issue, gsx-r', sv's... So it's COMMON, and really just takes slight amount of work to get it mostly sorted, and if you want it all gone, it's reasonably cheap to get the ECU flashed (IMHO, if you are going to go down this route, by a flashtuner, and then get someone to tune it for you on a dyno, as then you are not locked to a PARTICULAR person to do the tuning).
Yes aftermarket parts are limited at the moment, but it's getting better!
K&N said no we are not doing filters for your bike.... guess what we have them!
The good thing is quite a few GSX-R1000 parts fit our bike, so we can always use aftermarket parts for theirs on ours (springs, 2009-20014 air filters, levers, etc etc).
Anyway, TL;DR, there aren't any show stopping issues at this point in time, and with a bit of money spent on it, the bike is an ABSOLUTE monster in terms of power, with only just the exhaust done, and dyno tune.... can't wait till i get my suspension sorted for me.