At the moment it's turned the game from being pretty micromangement free in terms of economics (Note: I hate micromanaging economics), into a nightmare of screwing around with finding where I've got buildings turned on on planets, and generally pain-in-the-ass fiddling around with production queues. Take for example the following very, very, VERY common task in my current (sometime around the 9th or 10th try) at an AI10 game: I need lightning missiles.
Previously: I have lightning missiles in a queue. At some point it finishes, but I don't need one yet, and I'm running under the 15k a piece, so nothing happens. All is good since there's a 100% completed missile just waiting for me to need it. I decide I need it, I hit the "pause all" button, it stops all production of my ships all around the galaxy. (Yes, I do actually have ships being produced on planets other then the one or two main ones to pump out offensive ships.) At some point in time soon (a minute or so usually, it's pretty easy to estimate since I've got a little number underneath that says +X/second resources), I have greater then the 15k I need, so I hit "pause all" again to un-pause, and out pops my nicely completed Lightning Missile (or it could be a scout cruiser or whatever, I tend to produce all big ticket items like this).
Currently: I have lightning missiles in a queue. Except they may or may not be producing at any point in time, since I may or may not have positive resource balance, so I have to hunt down as to what's chewing up my resource. There is no easy way to do this, especially since it may be being caused by a random starship factory I took over in another system a while ago, and I set it to producing a couple of starships then completely forgot about it, or another of my missile manufactories building another missile. I don't know, and I have to find out because I can't just hit "pause all" and let it do it's thing. Usually this isn't a problem since it won't pop the ship out until I have a healthy chunk of resources, but since it's currently a continual drain, I have to track the damned thing down.
This is only going to get worse if it gets changed back from the current rather, well, boring method of having ships only cost one resource or another, since suddenly you'll have to micromanage every one of your docks, etc.
I like the concept of this, but it's really not working for the game since it's currently built around the previous method, and it doesn't have the dozens of buttons needed to "pause all but <thingie>" so you can actually play it without it being a economy-micro-lover's dream.
Also I never had a problem previously with estimating how much resources I was using. I used to glance at the numbers at the top of the screen enough that I could tell if the metal/crystal were trending up or down, and I could alter the number of crystal->metal converters I had enabled to compensate. Now I've got a "trending" number and a random flickering other number that tells me, well, pretty much nothing that I didn't already know. In addition it removes the actual useful value of knowing how much resources I have coming in per turn, so I can calculate how many turns it would take to get X amount of cash when I hit "pause all", which is important for things like dropping down buildings and the like.
Sure I can currently hit "pause all" and find that out, but instead of having two separate numbers that told me useful information, I now have two numbers, one of who's knowledge is completely redundant because I can get a good enough feel for it from the other.
IMHO, to use Revenantus' term, it's "inconvenient" now, and worked well enough before not to cause me problems.