Well, I finally finished it the other day.  I would rank the trilogy as follows:

1. MP1
2. MP3
3. MP2

MP3 is a very good game, but it falls short of greatness due to the increased linearity, heavy-handed story-telling, and inverse difficulty curve (it gets easier the farther into it you get -- I thought MP1 was ball busting and MP2 was insanely frustrating, but by the end of MP3 it's a complete cakewalk).  That said, the game is quite fun, and I can't wait to see how many units it's racked up by the end of the year.

It should also be quite interesting to see what Retro will do next.

I liked MP1, except the very end as you are ascending to the final boss.  Trying to deal with Metroids that can only be damage by one beam while jumping on platforms trying to get to the top door is very frustrating.  It was too hard.

I didn't really have a problem with MP2.

MP3 is definitely easier than the other two and more linear.  The story line adds more depth to the Metroid universe though.  Instead of Samus' computer dropping hints in the first two games, the hint system is now communicated through other characters.

Just finished the game - 99% (what the hell did I miss?) at 17:49 on Veteran difficulty. 

Overall, I'd rank Prime 3 behind Prime 1, but maybe a small notch above Prime 3.  I'm still undecided about that though.  Excellent game nonetheless.  Given the stiff challenge of Veteran difficulty, I'm sure Hyper Mode is gonna be really pwn.