I don't feel energy limits early fleets at all. In fact, unless you are playing 9+, it hardly limits much at any point in the game.
I know I have a VERY biased view on the game, but my opinion is if you are playing at 'edge' difficulty (Edge being wherever any particular player finds the difficulty balanced against them at) that you will eventually need more fleet than you have energy for.
Even if you simply consider first world builds, crank on a few starships and you'll hit base limit. Don't K up in manufacturies and you'll stall out your economy pretty heavily with heavy reactor builds, which is pretty easy to do if you start MK II'ing Bombers, Fighters, and special ship right out of the gate. It definately controls choices, since you can't feed the beast, per se, in the golden hours. At least not until you've revved up the AIP. After that I agree, it's golden hours only for that limitation unless you're playing low AIP (or medium golem) games... which is a different discussion.
1) It is tied to other resource system (it reduces m+c income) making it hard to balance independently. It is effectively a derived resource so it can't ever be a separate balancing lever.
This I agree with. One of the reasons I would like to, eventually, unhook Energy from M+C is I'd like to discuss a series of tweaks to the M+C system eventually. Right now it's a feast or famine kind of thing. I have a few core ideas on how that might be able to be better balanced but it needs to be a unique component centered around construction only. But well, that's a long term discussion.
2) Energy is only a problem when your fleet gets larger. To get a larger fleet you need to capture an ARS or research a higher Mark of an existing ship type. Research costs Knowledge. To get Knowledge you need to claim a new system.
Actually, you don't. K-Raids and spire Archives. But I know I'm splitting hairs on your point with that...
So nearly everything that that increases your need for energy also provides you more energy. As a result, energy is only a problem when you start losing system, it is never really a general concern.
I semi-disagree. Special operations units (Mob of Science IIs, Transport Herd, Cloak brigades, Fortresses) all outweigh their energy concerns compared to the affect they have. Fortresses are a good example. At 90k in Energy, and 3000k in research, for your one planet worth of gain (125k in energy, 225k at double reactor and 20% loss of conversion) you're using up 2-2.5 planets at double reactor worth of power. Throw in a stack of transports simply so you can get your scouts out that much further and you're looking at a massive energy spike with no compensation. Investing a K worth of knowledge into a few turret upgrades can have a similar effect.
However, once again it all comes down to system loss causing the issue, because the simple fact is you can't build what you can't power. Thus, Energy takes on a 'defensive failure' mode because FFs are the first thing to go. Now, you can micro around and start de-activating your fleet to bring your brownout back online, but the end result is the offensive 'push' of the forces (that you're maxxing energy out creating ships) is causing the defensive cascade.
I personally would prefer to see a system that avoided the resultant micro which would have the same effect as the end of the micro: Half your offense is left powered down and on automatic pilot for a home system because you needed to bring your defenses back online. Thus that whole control mechanic theory. Now, I agree, the complexity of it is probably a bit much. I'd hate to introduce another black box mechanic like firepower, but it's a brainstorm only.
To improve the energy system, I would consider the following:
a) Remove the m+c cost of reactors completely and cap the number of reactors in a system.
b) Re-design Reactors to work like Command Stations. There are multiple types of Reactors, each with pros and cons.
c) Powering down ships no longer reduces energy consumption. It still has all the other effects (such as dropping shields and holding fire).
d) Re-balance energy costs, in particular for turrets. It may be ideal to pull energy costs from turrets entirely, or maybe to just 10% of their current values. Push the offensive unit energy costs up to compensate, making low energy ship types an interesting strategic choice.
I personally like options A and D as a starting point. I'm not particularly fond of C simply because of golems and their need to repair. It's nice when you can 'swap them out' while one repairs and another heads back out with a rebuilt fleet.
Ideally they should have a restriction on being placed too close to each other, with the goal being 3 could just barely fit in a triangle under a Mark I Force Field, but that really just makes defending them more interesting.
The problem with that is because of the spacial concerns, nothing else would fit under the FF. You'd basically just always end up with a multi-FF system on any planet that had to defend its reactors.
Basic Reactor - Reasonable health, no armor. Generates 60k energy. This is the balanced middle-ground reactor.
Armored Reactor - High health and armor to survive repeated attacks. Generates 48k energy.
High Energy Reactor - Very low health, no armor. Generates 72k energy.
Stealth Reactor - Low health and cloaking. Generates 40k energy.
Home Reactor - High health, no armor. Generates 72k energy. Cannot be built, player starts with three in their home system.
Hrm, that's definately interesting. It doesn't necessarily break the energy mechanic off in general though. Here's one of the things that bugs me: If I'm building a Military station, why is it soaking energy off the reactor? Doesn't it HAVE one? What about the ships? Don't they have engines?
Now, in theory we could simply call Energy something else, Manpower or Communications, and it'd be the equivalent effect, but these should, to me, all start at the command station, not attachments to them. Hrm, I'll have to ponder that a bit.
EDIT: I should mention one of the reasons I like the distance decay mechanics is because it brings raids back into the game not because you're forced to, but as an option to mass-walking your fleet to a target and taking supply points along the way. I'd really like to see a way to bring some guerilla tactics back into the game. Right now the fleet-ball of doom with minor-micro is optimal to a huge degree.