A lot of stuff on the F-14 in here...
Politics aside, the sad truth is the withdrawl made sense with the way things were going for the 'Cat. If you remove such a large fraction of a given fighter commodity aboard a vessel, logistical support becomes a major problem. Those F-14As were inherently flawed because of the engines. Iran still has the F-14A, but despite any upgrades to the avionics/fuselage, I believe their fighter still has the original dangerous engines. Now, politics are ultimately to be blamed for its removal from service (war and politics, is there a differance?

), but remember the 'Cat was first put into service in '72.
In terms of "which was better: the Tomcat or the Eagle," it really seems to come down to preference and experience. Pre-Revolutionary Iran had test pilots fly both of the fighters and said the Tomcat was the better of the two. Iran also supposedly pumped enough funds into the program that it was able to be a success for both the US and Grumman. Israel liked the Eagle. But look at the geography: Iran is a big area, Israel not so much. Thus, if you've got a large area you need a large fighter with a powerful, long-range weapons system (F-14). If not, a smaller high-power performer will be perfect (F-15).
In terms of maneuverability, it depends on who you talk to, the condition of the aircraft's weight and balance, etc. As a cadet, I had the opportunity to speak with a former F-14 pilot. He said the aircraft was superior to the Eagle, and I'm inclined to agree with him.
As far as other aspects go, I'd actually suggest reading Osprey's "Iranian F-14 Tomcat Units in Combat." As with all things involving sketchy governments and thus having to resort to personal interviews where the interviewee is given a pseudoname, take it with a grain of salt. It's still a good read (short, too). If you don't believe the weapons system was up to par (there was someone who was suggesting earlier that the Pheonix was not too good a weapon), this title might change your mind.
If it still had a shot at an upgrade, the F-14 would be most impressive. The D model was great as it was, but an upgrade after that would have seen an aircraft imaginably better than the F-15E, at least in the low-level role. I think this would have been a more suiting end for what might have been the most iconic fighter to see service in the last 30 years...
-Thaeris