Generally speaking, I enjoyed Alias all the way through. I liked Lauren, too, but my understanding was the network felt audiences didn't like her, hence the rather sudden kill-off.
But after a fantastic first season, I felt the show pull away from what I liked about it starting in Season 2. For one thing, Sydney became a killer. That sounds weird to say, but the fact is watch those first season episodes again, and she does come off a somewhat of an innocent. That doesn't mean her hands are completely clean, and often it's only because her partner does the dirty work, but I liked how the show often found ways for her to use her brain to get around adversaries rather than pulling out her gun all the time. If you watched through Season 3 you know about some of the stuff Bristow did as Julia; it would have made more of an impact to see her "complete her test" if she hadn't probably been offing people left, right and center since the start of Season 2.
It also lost me for a while after they prematurely ended the SD-6 arc. That was, my understanding, pure network interference. And no amount of Sydney-in-lingerie can make up for the fact the arc should have run to the end of Season 5, or at the very least been resolved in a more satisfactory manner.
They also forgot that Alias is a science fiction series. All that prophecy stuff, etc. It was basically entering Fringe territory at times. They forgot about all that for a while and it basically became a La Femma Nikita clone. Which is great if the character is introduced as a bad ass from the start, but Sydney wasn't, yet instantly became one between seasons, without an event or epiphany that changed her personality, which at least would have explained it without violating the character's own internal logic.
Without spoilers, they did finally start to get back on track in some areas in the final season. Adding Rachel Nichols helped because it brought back some of the "innocent agent" aspects that worked so well in Season 1. But I do feel that Seasons 3 and 4, in many respects, were lost opportunities. But the basic concept as introduced in Season 1 only had a limited life expectancy anyway. This would have been so much better a show if they'd just produced a single 22-episode season.