Now, this is just my take on the issues...
RCCs are very necessary and practical for Riggers, even as they are.
It's a networking device which allows you to provide your drones with a better Firewall than they have on their own.
The networking also facilitates quick transitions between the drones you're *Jumped Into* since it only takes a single action to move between. If it weren't for the RCC, it would take 1 action to get out of one, and 1 action to get into the other.
And then there's the Noise reduction and Autosoft sharing.
I do agree that the Swarm program is rather wonky, since it doesn't require using the same type of drone. You could make a swarm of Fly Spies and Ares Ventures and they would all work together? Even though some are insects, and some are vehicles?
But at the same time, if you make everything compatible with everything else, then that's exactly what you'd get. Either a bunch of VTOL fighter jets trying to move like bees. Or a bunch of bees trying to move like fighter jets. I think it's better to leave some distinctions between them. A Rigger can own as many drones as they want, they don't necessarily need to deploy all of them at every opportunity.
1) Program Slots - This is kinda how most GMs I know handle it. Except they don't do shared slots. Especially since your count is way off. If you had 5x omni slots, and 5x more Auto only slots... but you can only share out 5x Autos at the most. You may have missed Core pg 223 (understandable since it's in the Matrix section).
So where do you store all of the things you want to keep? Pictures from your Aunt Edna’s wedding, credit information, your SIN, every book and movie you’ve bought, all the programs you might want to run—all of it fits on your commlink (or cyberdeck if you prefer). In fact, every device on the Matrix has a massive amount of storage space, unthinkable amounts by early 21st century standards. Your gamemaster might decide that a device is too small or low-grade or a file so massively large that a problem comes up, but such problems are extremely rare. Even if it does, the entire world is wireless, so you shouldn’t have trouble finding an alternate storage location.
You can store as much as you want. Meaning you could buy every Autosoft out there and keep them all saved to your RCC. The slot counts are just for how many can you have RUNNING at any given time. And since you can only have up to 5 shared out, then you can only have up to 5 running at a time. Which is why most GMs just say you have (DR) worth of Program slots, and you have (Sharing) worth of Autosoft slots, depending on how you have Noise / Sharing arranged at the time.
2) (Speaking of) Sharing and Noise - You already divvy out DR worth of points between the two, so that's no different. Although this new leaning towards swarms is going to force the battlefield more than adding swarms may be already. If you only need to share out 1 set of Autosofts to the leader of the swarm, and they will share it out further with the rest of your swarm, what you've done is create a subsection of your PAN. You're networked with that single drone, and it's networked with the rest of the swarm. Networks within networks, which most GMs frown upon. Same reason why you can't Slave all the team's Commlinks to the Decker's Cyberdeck... and then have each teammate Slave all their individual gear to their Commlinks. The Firewall and Sleaze protection doesn't cascade down like that, which would mean that all those guns and cyberlimbs are basically undefended. Or... you're totally circumventing the whole reason why the game says "only Device Rating x 3 devices can be Slaved". You can't branch 18 devices off of 18 more, and 18 more... So no, I don't think this swarm sharing thing should happen. It's just going to encourage Riggers to rely solely on swarms in combat. Instead of deploying a couple Roto-drones with good armament and good Autosofts being shared out... every Rigger is going to use a couple swarms of drones and overwhelm the battlefield. At which point the GM / Corps start using "escalation of force" and come in with their own swarms of swarms. And pretty soon the Face, Mage, and Street Sam are all dead b/c the only way to fight back against the Swarm Rigger was to nuke the city from orbit (it's the only way to be sure).
If you leave Sharing the way it is, it naturally imposes a limit to how many drones the Rigger can deploy at once. Which in the end, keeps the game balanced so it doesn't get out of hand.
3) Silent Running - As much as that sounds like a good idea, you're forgetting that Riggers aren't hackers. They don't need to worry as much about Icons and Marks, when they can just kill the guy doing it to them. If you double tap the grey matter, the hacking stops. And if you can't tell where it's coming from, ask your team Decker. All that hacking stuff is his job anyway.
4) Cloud computing and Swarm Intelligence - I like both of these. As you said, simply giving them Pilot (DR) seems lame. Suddenly, the RCC is doing all the work, and the drones are completely reliant on it. With your programs, they're still doing most of the work, and maybe relying on each other, or outsourcing a little bit of the work back to the RCC. But it's mostly the dog-brains doing the work.
5) Clearsight - I suppose you could make it a universal Autosoft. But then you've got combat drones wandering the battlefield going "I've got him in my sights! You're mine now sucker! Oh look, a butterfly!" =)
6) Smartlinks and Pilot Program limits - Now here you're limiting how awesome the Pilot rating can get (up to 6 even with help), but you're also trying to make them better fighters by giving them Smartlinks. The way I've always seen it... the Smartlink HUD and the Targeting Autosoft are basically doing the same thing. Using a computer to take environmental data and calculate the best trajectory for shots. So you'd be giving them twice the computing on every shot. I think Smartguns should only be accessible to the Rigger if they *Jump In* to that particular drone (and obviously the Rigger needs a Smartlink implant). It gives them a little more motivation to do so, instead of sitting back with a beer and a slice of pizza, watching the drones run around the battlefield all willy-nilly.