I would agree that the first half of the show felt like it was building to something big and meaningful and the second half didn't pay off nearly as expected, but at the same time I can't say I didn't like what we did get and don't appreciate it. All in all I think it was a good show and worth the time spent watching and thinking about it.
After a lot of pondering and trying to look back on the show through the lens of the first episode as the final scene reminded me to do, I realized that the only characters that really grew or changed in the whole series were Akane and Ginoza. When I think about everything that happened in just the terms of those two I find I like the show overall a lot more. Makishima and Kogami were like avatars of different ideologies fighting it out the 'old' way and while their battle was intense and interesting ultimately it was a traditional example of two sides who want opposing things battling it out the traditional way of get him before he gets you. Where the goods of the series seem to be though is in seeing how Akane and Ginoza, as products of and proponents for the third option represented by Sybil, dealt with and were changed by interacting with the traditional bad guy role played out by Makishima and the traditional good guy role taken up by Kogami.
In the end Akane was not tempted into taking up one of the traditional sides and maintained her dedication to the third option despite much loss and angst. I'm not sure how to read Ginoza's shift but I'd like to believe that despite his crime coefficient going up he still believes in the ideals driving third option and is willing to help enforce them, but he's just become too aware now how ugly the world that the system is trying to cover up is to go back to just being another cog in the machine. Maybe he has the potential to become the another rogue like Kogami, but my hope is that he's become closer to the ideal Enforcer who can't be a part of the system proper but can still protect it from others who want to go against it.
And then in keeping Kogami alive and free I think they were throwing a bone to the notion that as long as the system isn't perfect and people like Makishima can pop up you'll need Kogami's out there as well to try and counter them.