Here is the last few Honda Cr250R engines in a nutshell
2000- Considered the best CR engine by some, broad usable power in a very stiff and unforgiving frame, I rode several of the 2000/2001 and liked the '96 steel framed CR's better.
2001- Same engine but Honda makes the first in a series of blunders with the CR and swaps the Keihin carb for a Mikuni. Honda will stick with the Mikuni, both without and with a TPS for the rest of the CR production run. The Mikuni carb is the weak link in my 06 for sure, Honda must of had a warehouse full of these.
2002-04- First year of the case reed design and all new electronic powervalve and much better alloy frame. The bike has good HP numbers but never gets that nice low end bark back. Minor engine changes frm 2002-2004. All development money is going into 4 strokes after the CRF rolls out in 2002.
2005-2007 New cylinder and one piece powervavle design, much better sealing than old two piece design, Mikuni gets YPS and despite a bunch of changes the motor is at its peak of development and still doesn't have any low end.
The 2005-07 engine is the most technologically advanced 2 stroke engine Honda has ever put in a motocross bike. Is it the best? Who knows. It certainly has a lot of potential for improvement in any case as countless builders both in the cart and motocross world have proven.
MXA was asked about the 01 vs the 07 CR and the gist of their reply is that although they liked the 01 engine better (AKA Service Honda) they would race the latest version (07) beacuse of its superior frame, handling, ans suspension and the bike is a newer design. They also mentioned the Service Honda as being the best of all worlds with a 01 engine in an even newer late model CRF frame and suspension.