I loved season three of Ent, I also think that while season 4 has good material in it, as a whole its rather weak, as it utterly lacks focus, and lunges from one arc to another, not given characters and situations needed time.
As a whole I think season 3 of Enterprise is better then any season of Voyager, better then all but seasons 3 and 4 of TNG, and better then all but seasons 4, 5 and 6 of DS9. I think season 5 and 6 of TNG (are it's due to about 6 episodes in each of those seasons that I rank blow average).
In fact I think season one is actually better as a cohesive whole, then season 4.
I think because so much of season 4 is (at least to me) basic fan wank (even if enjoyable fan wank), really, really hurts it.
Frankly I really, really like season one, which is easily modern Trek's best first season (easily).
The idea of a crew that initial runs from a threat (I loved that), a crew that we see rush out to see things like a comet, a planet, ect. Having the ship do PR message for home (just like NASA does). There is no Trek show that has ever managed to captured that wonder and newness, or even the terror better.
Heck people bitched about the episode that the Crew discuise themselves as natives, they said its been done before. Well of course it has, but it had to start at some point. I loved that. I love the joy of seeing a ship or how similar they were, the delight the crew had to the outrage they had at an advance race willing to kill them. All things that by and large are glossed over in all of Trek, even in TOS.
The downside are some rather small but hugely annoyingly things.
Cloaking devices. AARRRGGGHHHH. In the pilot Reed says he sees it briefly then instruments fail. That was perfect, a complete way around the cloaking device. It doesn't become invisible, just invisible to sensors. Space is huge, unless a ship is right next to you, you would never see it (especially in deep space. But no, once the term cloaking was used, they went (season 2) for the full on invisible, huge, huge, huge mistake (and one so easily avoided).
Mayweather. Seriously, seriously the actor might be great, but the idea of having the outside, the one who's lived his whole life on the edge of known space, as the most well mannered, easy going perfectly groomed person was a huge, huge mistake. Mayweather never, recovered as a character.
Archer, sorry but as a Captain he by and large was rather bland. But like Sisko the character with time did come alive. Archer needed a spark lit under him, Sisko needed to shave his head....
Using the Ferengi first season, while the episode isn't terrible (it's actually one of the better Ferengi episodes, certainly the best none DS9 Ferengi episodes) and technically without a name given there is nothing for Picard or Data to match to the name Ferengi (as they have no visual records of that race), its still a huge slap in the face to fans, and was a terrible choice.
Besides a few episodes that just for whatever reasons didn't work for me Rogue Planet (just boring), Terra Nova (Great concept, perfect for Enterprise, yet yuck), Unexpected (sorry but I like parts of the episode, but the heart of it, I found rather juvenile), and Fusion (another episode that not awful just bored me). Otherwise everything in the season is good to really good to me. It really wasn't until season two that I started actually seriously disliking some episodes of ENT.