Yeah, I don't use the AXE as my interface since I am doing other things in PT. Honestly, I've tried every configuration in PT even when I had my ULTRA. The converters in the 002 are awful so I used to go Line Out (ULTRA) into a Lavry AD10 then went SPDIF into 002 / PT 8. Which sounded really good. I was recording using SPDIF. When I upgraded to PT 9 the Axe II arrived so I thinned out most of my gear and bought a solid audio interface (Metric Halo) because I am tracking and editing off a macbook pro (FireWire). The issue was then latency because of the monitoring issues not worked out yet in PT 9 and third party gear. Upgraded to PT 10 and now toggle to the Metric in the playback engine and have Metric's Mio mixer open. Haven't had an issue in months and the tone is incredible / very open sounding then going direct with Axe in PT. Definitely noticed a difference A/B'd.
Honestly, with the 3.02 update, if you're not liking the stock preset sounds in Bank A something is up with your setup. Could even be your monitors or headphones. The stock sounds are that good and especially if you strip any effects it should still sound incredible. Also, follow Scott Peterson's how to for 3.02. Good luck!
Note: If you're using OUT1 to monitor then raise your levels for each preset if the rec level is too low = Mixer Level (amp block).
* Gain, Volume and Mixer Level will be different for each amp/preset and obviously should be used as well to tickle the red then rolled back slightly. I would work on just barely hitting the red in your Axe using the gain, vol and mixer level and then watching it barely hit the red in your recorded track in PT. The Axe Wiki and Scott P's notes saved me so much time. They're both very well written.