Here are my thoughts on this...
1.) I agree the zig zagging to go in a straight line is kind of ridiculous, I know it is because of the hexes but it still seems a little silly and offputting.
2.) I have not really noticed this so much, must be lucky I guess, then again I do not spend much time all the way zoomed out, I prefer to look at the visuals up close, which look very nice so far.
3.) I have done two complete plays through the Alpha and colonized and conquered many worlds and never saw this issue.
4.) I find that the bonuses are completely different for the same icon then they were in GC2 it took me a little while to get used to them, though I do like that most provide more than one bonus, but nothing provides more than +3 in a specific category, what about precursor factories or libraries? Will those be making a return I remember them giving a +700% to production and research respectively. It also seems that more than half provide an economic bonus while only one or two provide a research or production bonus, this seems like a major departure from the bonus system from GC2, just an observation.
5.) I strongly agree with making auto update a feature again if it isn't going to be already, I find it more than a little tiresome to cycle through all the planets to upgrade buildings once the requisite tech is researched.
6.) I also find it a little annoying that certain improvements cannot be upgraded (market centers, farms, ideology based influence buildings, and ideology based special buildings) and must be destroyed prior to make way for the clearly superior building of the same type. I also found it a little peculiar that the enlightenment center costs less to build than the missionary center for the benevolent ideology when the former is clearly a superior building and by the logic of most buildings should cost more, just a thought.
7.) I do not very much mind this, it could be explained by the lighting (you know because Cardassians really liked deep blue lighting for some reason, maybe the Altarians have developed a similar affinity?), or a the result of some species wide genetic mutation, or even a massive species wide re-pigmenation project because blue is cooler I guess...? Either way an explanation to the new altered Altarian appearance might help with credibility of them being similar to humans, but not really. Either that or change the race description I suppose, it does not really bother me just making some suggestions to fix this for those that do...
8.) Definitely agree with this and mentioned it in another discussion topic.
9.) I think that this is a welcome new addition as you can select continuous production on wealth, research, population (not sure how that works exactly, cloning I guess...?), culture, or some ideology based production to keep those planets busy that you have nothing else to do with. I think this is far more preferable than the alternative which is to have them do nothing and waste all that spare production every turn.
10.) This reminds me of setting research focuses in Alpha Centauri I liked that feature, kept me on my toes because I did not now what new technologies would be discovered next! I still think it would be good to set a focus though so the feature can be tailored to a particular play style (i.e. quick expansionist, research heavy, military domination, etc...). Could also be helpful to new players that might be intimidated by the tech tree or players that would rather focus on something else. Again just a thought take it as you will...
11.) I noticed this in very high instances as well, it was either this or the precursor ship. I know this is just the Alpha and from what I remember from GC2 getting the research pods was far more likely than the precursor ship which rarely if ever happened on a play through of a large galaxy in GC2, so this is probably just a case in which there are currently only two random colonization events with the pods being much more likely than the ship. I am sure that this will cease to be noticeable with future updates as the development team will likely add all the random events from GC2 back in and add some more to boot! On the topic of random events I wonder if there are plans to implement galactic wide random events like in Endless Space, I think that would be a nice feature if not already in the works...
I know this is long but I noticed quite a few things that I have a fairly strong opinion about or just wanted to put my input in on. Hope this helps the development team I really appreciate the work you did on the Alpha and think you sell yourself a little short when you say it isn't fun, because even in this early state a thoroughly enjoyed my play throughs and eagerly await the release of more features to give it the depth and polish the game deserves. I hope I have not come off as mean spirited or condescending because my intention is anything but. I greatly appreciate the work done so far and the promise the project holds.