Never driven the CAT 3000 but own a CAT 2000 '98. The CAT 2000 series (e.g. original, EC, SE, 98) and the CAT 3000 (aka CAT 3K) share many parts.
Regarding performance, the following posts may be helpful as they discuss the different versions of the CAT 2000 (e.g. original, EC, SE, 98) and the CAT 3000. Additional posts can be found on racing-cars.com, Oople, and RCtech.
Oople.com: CAT3000 racer.
http://www.oople.com/forums/showthread.php?t=47339&highlight=CAT3000+racer
Oople.com: CAT 2000 - Which chassis
http://www.oople.com/forums/showthread.php?t=3173&highlight=2000+chassis
Ooople.com: Which CAT 2000 for clay track ?
http://www.oople.com/forums/showthread.php?t=108545&highlight=2000+clay+track
Based on the various forum comments, the CAT 2000 series were generally held in higher esteem. However, local track conditions seemed to play a role in the different opinions. Notably, the CAT K1 and K1 Aero use a layout more similar to the CAT 3000 than the CAT 2000.
There are comments about rear belt skip (due to less pulley wrap) on the CAT 3000 and modifications (search RCtech) to secure the rear arm mounting blocks. Do not recall similar comments with the CAT 2000 series.
CAT 3000 rear belt skip is mentioned here on racing-cars.com forum
http://forum.racing-cars.com/forum_posts.asp?TID=15102&title=cat-2000-questions
The CAT 2000 SE and '98 use the same universal joints, pulleys, and diff outputs as the CAT 3000. Uncertain if the differential housings were rotated off center the same amount. Some key differences between the CAT 2000 series and CAT 3000 series include:
motor position and layout
the manner in which the top deck and the shock tower mounts are secured
rear arm mounting method (U1434, U1489, and U1490 versus U1984, U1987, and U2253)
a narrower front U-bar (U1484) on the CAT 2000 series versus (U2276) on the CAT 3000
different shock tower options (to mount longer and shorter shocks) for the CAT 3000 (presumably to support different track conditions).
Page 14 of the document linked to the following post may help when comparing the different models. It has links to many relevant exploded diagrams within the pdf.
http://www.rc10talk.com/viewtopic.php?f=28&t=28751#p447564