I actually think "The Two Doctors" is highly underrated. It is one of my favorite 6th Doctor stories. Is has a message to it (whether you agree with that message is another matter, but I always give a point or two for true sincerity and an attempt at substance) and a plot that actually makes sense without a lot of dull plodding that pagues oldWho.
Best of all, the story comes first and the fact that there are two Doctors comes second, a real smart move. Just like how "Caves" wasn't so much about the Doctor regenerating as it was about its story, with the regeneration secondary.
This is how it needs to be done but probably won't. Just like "The End Of Time" was pretty much just two-hours of ZOMG David Tennant is LEAVING....and oh yeah, dull plot with cactus aliens and a rich black guy that quickly gets forgotten, I have a feeling that the 50th and Matt's final episode will be "Multi-Doctors!" and "Regeneration!" first and story, if any, second.