There might be some incompatibilities concerning animation internals but as far as modeling goes you can model in new version and get it back into 2.49 if you use Legacy option while saving project.
If you are already familiar with how to work in 2.49 there is really little to no difficulties to switch over. Just a matter of a bit exploring around and getting used to the interface, main arguing point being horizontal/vertical tool shelf change.
Some quite cryptic named 2.49 interface elements are mostly named fully, which means they could be found.
Spacebar Help - brings on text field you write some letters and are given the list of commands containing those…
There is little help material left on the internet to 2.49 while for the 2.5 and 2.6 you’ll find plenty.
I had 2.49 lying around almost never being used but after changing my OS to the newer one month or so ago it’s not there anymore.
There are some forum members still using 2.49 - McThingy being one of them, i guess- try to PM them if there is no answer on the Internet and you still don’t want to switch.
That’s about it in my pros list and i really have too little legacy to name a lot of cons.