OK, here's your answers (all specific to what is coming as of the 1.4 release due NOW):
Production Overflow: already exists. Has since the Alpha. Works the way of your first proposal. To see the overflow amount, simply hover the cursor over the Production Queue area. Yeah, not terribly intuitive.
This also works the same way for Production allocated to Shipyards.
Decay won't happen. I don't expect it to ever be popular enough to be included, because it's pretty useless as a mechanic, simply because it's hardly ever encountered.
One annoyance: the Production Queue estimates how many turns it will take to build the structures, WITHOUT taking into account Overflow. It's been complained about, and it will probably get fixed in 1.5 or so.
Research Overflow also happens already, though it's hidden even more. You don't know how much there is overflow, and it doesn't show up on the initial estimates of time to research, but it absolutely is happening. To see it visually, click on the technology that is AFTER the one you're researching. Continue researching until your current one is done. The excess amount will automatically (whether you want it to or not) roll into that successor Tech. If you don't do this, and instead just select techs, when you finish a tech then click on a whole new one, the overflow simply will be added to your first turn of research.
Micromanaging is over. The Wheel and Slider for each world is GONE, NEVER TO RETURN, as of 1.4. Thus, give up on getting exact values to match production to buildings/ships. It's for the best - micromanaging to get ships/buildings in exactly the right amount of time for each planet is a waste of time, and seriously hurts game play. The global wheel could possibly be better refined, but it works well enough for now.
Economy concerns: I doubt you'll get support from the rest of the community for sound-effects on production wheel changes. Personally, that's something I think is really annoying. It also doesn't add anything to the game, other than personal preference (i.e. you like it, I don't, but it doesn't add any definable benefit other than aesthetic), so it would go waaaay down on the TODO list.
Again, the per-World Slider is GONE. "Focus" (like in GC2) is now the name of the game, along with using "Super Projects" to transfer Production to Research/Wealth on a per-planet basis.
There are Governors coming, which will include customizable governors: i.e. ones which have specific build orders and allow for Focus and Projects. Right now, they're kinda primitive. They should get better by 1.5. But remember: There's no Micro for planets anymore, so all a governor has is a build queue and Focus ability, and can't set Production/Research/Wealth directly anymore. It will be possible to set multiple planets to use the same Governor type, of course.
You can sort planets by the amount of any column you see in the Govern screen (by Production, Wealth, etc.). Right now, there is no "grouping" ability. There may or may not be one in 1.4, but probably in 1.5, along with the ability to group by Governor used.
Research View: yeah, zooming would be nice. The current presentation emphasizes the "Ages" concept, but it's a bit annoying. Don't have any ETA if this is going to be changed.
Seeing the entire tech tree probably won't happen. Other than "wow" factor, why would you want to? The techs aren't inter-related, and it takes a *lot* of screen real estate to show that big of a tree. Panning around the tech view in GC2 was a PITA, and GC3's categorization makes the interface cleaner, IMHO.
The tech variety WILL be improved, but it will happen slowly, over time, and probably will include some only available in DLC or Expansion Packs. Mods will also be a great source of variety here. Frankly, this is something that has great potential, but it's a *lot* of work to get right and balanced, so I completely understand why it's essentially a "no frills" version right now.
Ideology: yes, colonization is the primary giver of Ideology points. This is slowly changing, as there are more and more Galactic Events and Anomalies which give Ideology selections. Also, the various Ideology-generating buildings are undergoing change, as is changing how many points are needed for each advancement based on mapsize/planet density. However, it's NEVER been the goal for a game to have more than a dozen or so ideologies attainable. "Collect them all" isn't the point - you absolutely MUST be selective about which you want.
The choices are undergoing continued balance, as we move forward. The current set is better than it was several months ago, and should improve over time. That said, give that you MIGHT be able to get HALF of any one specific Ideology, the current "balance" isn't so bad, since it's still far more important about which you chose, than the ability of one Ideology to have lots of nicer ones than others. Also, the appeal of each Ideology's benefits differs based on your race and game: +1 colony ship may be *extremely* appealing in a game with spread out stars, while pretty useless in one which has dense-packed planets.
Hope that helps!