Personally I would go with QSS. It seems to fit in well with the Federation look and feel. Transwarp feels a little bit Borg (obviously).
Having dabbled with QSS in the past I should imagine the Federation showing some keen interest in further developing the technology upon the return of Voyager from the Delta Quadrant. I should imagine, like with any new technology, there would be stumbling blocks and the occasional accident but the rewards of succeeding would be well worth the sacrifice of the odd mishap.
Much like Warp Speed it would probably take decades to master, much like the slow but steady improvement in Warp technology from 1 right the way up to 9.975 over the period of a couple of centuries.
As stated in previous posts the main problem appears to be the lack of computing/processing power. The ships themselves seem to be able to cope just fine in the slipstream without disintegrating after a couple of minutes.
This is only my second post. Im like a fat kid in a sweetshop after finding this site :-)