It's almost time for a new expansion in The Old Republic, so I've finally finished the Makeb story line on a Republic character. I completed it on my Jedi Knight (Sentinel).
The new GSI buff stations that boost your gear level make Makeb much easier. I once accidentally logged out in the middle of a mission far away from a station, and when I logged back in I did not have the buff. The rest of the mission was much harder. I had to switch from a dps companion to a healing companion to finish it.
It's pretty clear that the Republic story line should be done first. It comes earlier, and a lot of the mysteries are cleared up when you go through the Empire story line. The Republic story is also a lot more straightforward than the Imperial story, being a regular rescue mission. Albeit a rescue mission for an entire planet.
The only hard fight was the final battle, and that was mainly because I kept getting one-shot right at the start of the fight. Once I figured out that I had to start the attack from a different location, it went smoothly. Of course, this probably more due to the GSI buff than any skill on my part.
I would rate the Republic story lower than the Imperial story. The Imperial story was a bit stronger, the NPCs (especially Katha Niar) were more interesting, and the conclusion was stronger. Plus Darth Marr is just awesome.
I think the villains for both stories were a bit weak. For one thing, they didn't really have any personal contact with your character until the very end.
Overall, Makeb was an "okay" story. Nothing really amazing, but nothing really wrong either.