Speaking as someone newer to the game, I don't really get the cloaking mechanics beyond "you usually can't see cloaked stuff, and tachyon whatsits decloak cloaked stuff within some range somehow."
This is a great point, I don't know that the specific cloaking mechanics are really explained anywhere. I've added that to my list to put into the wiki in detail, but here are the basics:
1. If a ship is cloaked, it normally can't be seen or targeted by enemies at all, not even the little purple circles.
2. If a cloaked ship fires its weapons, it becomes completely visible for around 8 seconds or so.
3. If a cloaked ship comes within range of a tachyon beam emitter, it becomes visible as a purple circle only, which lets enemy ships fire at it but doesn't let players tell what kind of cloaked ship it specifically is.
I'm a big fan of waypoints. IIRC, Total Annihilation had the most comprehensive waypoint system of anything I've played. It would let you form a multi-point patrol route, so your ships could patrol in a square or whatever, and you could combine other waypoints however you wanted with whatever you wanted. I might just not be remembering the ways to break it, though. 
I'm less a user of waypoints in most cases, but SupCom also had all of the above features (being effectively the sequel to TA). I really liked how it did patrols and such in there, too. But with the AI War model of movement and fog of war (per-planet, not based on smaller sight lines), it just didn't make sense to go too overboard with that as a feature. Also because there are typically fewer things you need to go around, no mountains or rivers or whatever in space.
You could also assign factories to a subgroup to have units built by that factory automatically placed in the subgroup, which was pretty cool.
Yeah, some other players mentioned this one -- I hadn't been aware of it. Since version 1.006 or 1.007 (I can't recall which now), this is also a feature in AI War.
One other very common way for waypoint systems to fail is to not give you the correct commands you need to set up all the waypoints. A common example is transports, like dropships in Starcraft. They have commands to pick up units and to drop off units, but the drop off units command is unavailable when the dropship has no units in it, which prevents you from setting up an order to pick up some units and drop them off somewhere else unless there's already at least one unit in the dropship. I'm pretty sure you also can't queue up dropping off one unit, or any number of units less than the maximum, but I could be wrong! (Ooh, I haven't seen the 1.007 transports yet! )
Yeah, I don't see the waypoints system in AI War ever becoming that robust. Simply because the interface and everything else is just not designed around that, I would have had to have that as a design assumption from the start, like TA or SupCom presumably did. I've really been more mirroring what you can do in games like AoEIII or the others, in general as far as waypoints go. Just based on the flow of AI War, it just isn't something I feel like will add a lot; most of the problems that are solved by waypoints in TA/SupCom are solved in other ways here (such as having constructors be cheaper, and not require upgrading, and quicker to build / build from, so there's no reason to have all your constructors at the back and ferrying things forward, etc). And there are other examples, too, but that's the big one.
The new transport for 1.007 is something that is really only intended as kind of an "armored shell" for temporary use to get past difficult planets. It doesn't have any of those automatically load/unload features of TA/SupCom, or any of the ferry abilities that were so cool in those other games. Here again, this one is just more of an ancillary feature for a specific strategic solution, not something that will be used in every game or on most planets. It makes me hesitant adding a feature like transports, when I'm adding them for one specific use, but people immediately have assumptions that it will also come with a bunch of ancillary features...
I think this one is tricky. I agree to an extent, but I'm not convinced this is really an "interesting decision" rather than a management tax. That will definitely depend on the player, but personally I think I'd micromanage away until I was just too sick of it to do it anymore rather than seeing it as a decision or tradeoff. With your perspective on it I might not, but I'm not even sure about that! 
That's a valid point, but I really see the "micromanagement tax" option as just being a one-off thing in a very occasional situation. Usually there is just not that much time available to spend on managing scouts to that degree (the AI is busily reinforcing while you're doing that, and/or attacking you), so it's just an end to check out a specific planet or two when it's really needed, not something to do overall. It's one of those cases where if you don't like the micromanagement, just get the better scouts (which is what is intended) -- if the lower-level scouts were more effective, there would be no need for higher-level scouts, after all.
Part of that is that I don't like losing the starships. I don't really mind sending the little scout ships off to inevitable doom, since I imagine they're robotic, but I imagine the starships as having all these little people on them and don't want to blow them up for no reason. I know that's sort of silly, but there you go.
I imagine most of the ships as robotic, but it's definitely ambiguous on purpose so you can picture it how you want. See this about Scout Starships, though:
http://arcengames.com/mediawiki/index.php?title=AI_War_-_Starships#Scout_StarshipsThat would make sense, but I'm not sure how intuitable it is. Of course, as you noted it doesn't really make much sense to have waypoints on other planets without a way to select ships on them! Maybe that's just something that doesn't fit too well with the current selection method.
Yeah, and I
really don't intend to change the selection method so that players can select ships on multiple planets at once. That would just break the feeling of separation between planets, in my opinion. I think it kind of makes since that if you have a "leave this planet" order, any other orders on the local planet would happen before you leave. It might surprise a few people at first, but hopefully that will be an easy thing to understand after the first time they see it. It's certainly a step forward from the current model, at least...
(This is probably obvious, but I love your forum's smileys!)
Haha, yeah, I like them too.
