Omni-radar like units are too powerful

My main issue with this is that I think it's non intuitive for the player, although if you have examples of what this might look like, I could be convinced otherwise.

I'm also worried about the game becoming stealth/cloak centric, but that may be just a balance issue.

Is it just me or is that not how Omni worked in SC:FA anyway. Build one, look at the concentric rings of different colours. Pretty sure that the different rings represented different things.

Did the commander not have a little yellow ring around him allowing him to see cloaked units within that ring?

I think the more experienced people here have already hit the nail on the head. it's all about proportion and scalability. If you want to make the technologies separate then by all means do so. The trade off with the Omni was that by destroying a single building you basically made the enemy commander "blind".

Made me think: I would quite like to see how the nuclear EMP effect could possibly be employed in the game to temporarily deactivate sensors indiscriminately over an area by detonating a nuke over the planet.

Ever play a game where the other player is hiding his com or last engineer?

I kind of agree with your point that balance for visibility is very important. And if omni radar is too good and too easy, that is kind of a big deal.

On the other hand, we're talking battles stretched across entire systems. It's going to hurt me deep inside if spy satellites aren't available, and realistically, they would see pretty much everything.

But I don't see any reason why spy satellites should be able to see through cloaking either. And I really would like to see some good cloaking units in PA. To deal with cloaking you should need more specialized and most importantly limited ranged units to counteract cloaking. That should not be so easy.

Also, spy satellites are by their very nature somewhat fragile. It shouldn't be too easy to completely dominate the orbits and gain total map vision. After all even inexpensive ground based rockets can knock out satellites fairly cheaply and easily. Not to mention ground based cannons or lasers or whatever other crazy things we end up having available to us. There should be a number of ways to attack orbital units because they are fairly easy to spot with simple optics, and have no choice but to be in fairly predictable places as well.