I liked the second. The first film was very simple, good guys versus bad guys. The humans were the good guys and the machines and their agents were the bad guys. The philosophy was nothing new if you've ever read Alice Through the Looking Glass and wondered about dreams and reality. The visuals all looked a bit dingy. I thought the early little drops about Neo being the messiah were tedious.
The second film is more complex. It's no longer a two-way battle. It's at least 3 way, humans versus machines versus Mr Smith, plus various other programs like the Merovingian and the Architect who have their own agenda, plus the Oracle is no longer human and much more ambivalent. The philosophy, although not necessarily correct at least now it's not totally obvious (about choices being predictable and the need to understand choices already made). The visuals seem prettier and the SFX more polished and assured. I liked that they faced up to some of the consequences of Neo being the messiah.
The third film loses it, though. Shame. The resolution is too mystical for me.
In some ways the first film is better cinema. The second film tenRAB to alternate talk-heavy bits with SFX-heavy bits, and I can see that would put off some people. Also, I think the philosophy in the first film was new to some people. So I can see why people like the first film, but the second film is underrated in my view.