Prinergy is by far the best, slickest and most progressive, it is more visual than others and if given enough CPU's is blisteringly quick, I have also used Apogee and Heidelberg's offering which is also very good (now). Stay away from Screen though, very poor and you will have very little say in any future development..
As far a CTP goes It depends on throughput, also if you do fast turnaround overnight work (NO FAIL) you will need two machines, all CTP devices/autoloaders/processors have downtime.
Thermal I believe is a must, for unrivaled consistency (Kodak or AGFA plates will be the best and depending on the amount you use you should be able to get a good price)
We currently use two Avalon XXTs running 42 plates an hour each, they are fitted with NELA autoloaders. Running over 100,000 plates a year.