Many Primes have a matrix but I assume you mean a removable matrix. Big Convoy has one and Universe Nemesis Prime has the dead matrix. THS -02 has one and I'd assume THS-01 has one since he is minature and more detailed version of cybertron prime
Masterpiece Prime is the Prime that ends all Primes. The movie, and Classics Prime would be ties for my second favorite Prime.
I'd have to say my personal favorite is Energon Fatimus Prime....just kidding. I really really like Cybertron Leader Prime. A strong look(exacting to the cartoon), a lot of features, and his ability to "power up" and to combine with Leobreaker or Wingsaber into different, more powerful modes is extra pluses in my book. I feel that OP with Wingsaber in Sonic Wing mode is one of the coolest, if not the coolest, Transformers ever made.