This is a complex issue, but since your just getting started out with Blender python scripting try and understand that the pre 2.5 API can only be stretched so far. Once you get to a certain point with it, things become very problematic. 2.5 will hopefully fix all these problems.
For what its worth, I have been maintaining thousands of lines of python code written for the current API in a production enviorment for several years now. I can tell you from experience that the current API can bite you hard in ways you least expect. Because of this I have no reservations about retargeting all my code for 2.5 because the pros definitely outweigh the cons.
Trust me, the changes being made here are the result of very informed decisions.
but yeah access to data will change and python will use operators “what blender can do python can do” but to cater for this major changes had to be done and they simply was not compatible with the old api
scripts will not be hard to port as the new api will be roughly the same in terms of syntax etc etc
So much of 2.5 python api is speculation and unknown at the moment so I cant give an answer on this.
Only think that may be of some conciliation is myself and others will be porting scripts to 2.5 so we will probably hit most of the the problems first - and resolve them.
There are 2 GSOC projects that will also be working in this area so the 2.5 api will be getting some attention from more people.