I am on turn 353 playing as the Mimot Brotherhood and I have a few complaints/suggestions:

1. When you successfully complete the "Against The Tide" galactic challenge the game should NOT automatically end your wars against all opponents.  It should give you the OPTION to end any wars you want to end, but let you continue wars you want to continue.  As you can see from the first large screen snapshot below, all I have to do is finish off the Terran Alliance to win a Conquest victory (the only one I have enabled) and successfully completing the "Against The Tide" galactic challenge ended my war with them and now I have to wait some unknown number of turns before I can declare war against them again.
2. When you get to the end of a long game and you have researched every technology, the "Capstone" technologies (see the second screen snapshot below) just keep repeating, but you do not get increasing benefits.  You need to come-up with something better at the end to make research still have some value.
3. You need to come-up with some better "Available Projects" that can be done on planets where all cells have been developed and all upgrades have been completed. Just loading-up the production queue with "Economic Stimulus" is annoying and sucks. Perhaps having a way to put planets on auto-pilot to produce something of value would work.
4. I do not understand why you have not incorporated the ability to demand the surrender of an enemy to YOU (not another AI).  The outcome of this game has been known since about turn 80, but I have had to slog my way through every sector completely destroying every AI down to their last core world.  The game should recognize when an AI you are at war with has no chance of defeating you and adding an option in the Diplomacy screen where you can demand their surrender.  Capturing every single planet is very tedious.
5. I enjoy surveying anomalies and seeing what "prize" I get with each one, but all anomalies are gone by somewhere in the middle of the game.  I think it would be a good idea to have some way of sprinkling more anomalies around throughout the game.  If players do not want to go after them, they do not have to, but those of us that do would enjoy seeing more of them.  Note:  I echo the complaints that others have posted about AI ships that do not have a survey module being able to survey some of the better anomalies.

Since I never like listening to people who just complain all the time, here are some of the things that I really like about the game:

1. I love the fact that I can setup the game pretty much any way I want:
   1. Who do I want to play as?
   2. How many opponents do I want and which ones do I want to play against?
   3. What kind of a universe do I want to play in (see the third screen snapshot below for my current choices)?
2. I love the first 30 - 50 turns where I get to discover what my surroundings contain.
3. I love the ability to choose what I want to build in my core worlds and in my shipyards to pursue whatever strategy and tactics I have chosen.
4. I love chasing after anomalies.  Each one is like a present I get to open and some of them are very valuable.
5. I love the progression in the game that lets me build stronger and stronger ships.

Keep fixing the bugs and enhancing the experience of the players and you will have a winner.  As you can see from this small screen snapshot, I have played this game a lot during the Alpha and Beta stages and, even with the issues the game has, I have found it very enjoyable.