I wouldn't want a system where doing subfactions costs points (especially for those players relying on them to manipulate battle line choices). Points really aren't the be all and end all solution to balance.
I understand that GW likes their current book format for rules (as they are very much near the base of their income pyramid), but because they keep up the (imo) antiquated battletome/codex format, these imbalances remain in print for a loooong time... They seem to want to shift more towards a living rulebook system, but as long as they are unwilling to do complete overhauls of certain bent/broken items in the allegiance systems, the examples you've given will keep on existing. BUT, I have to say, the latest Slaanesh tweaks make me hopeful that in the future, tweaking or downright nerfing allegiance abilities is also on the table.
Personally, I would like them to swap to an entirely warscroll based system for their rules (the whole lot: artifacts, spells, allegiance abilities, subfactions,...)
If one turns out to be a bit busted (like Slaanesh recently, or the the FEC savage strike, Petrifex,...), they can just bring out "update decks" for each grand alliance alongside GHB. Hell, you can even use to boost and change warscroll cards for the woefully weak elements in an army as well. This way, armies would not be left to linger for too long and your army would get more regular updates apart from some points adjustment.
Petrifex a bit too good? Swap a single card over next year to tweak it. Hag-nar head and shoulders above the rest? Either change Hag-nar or buff up the others to make them more desirable in stead? One magic item is stacking a bit too well with a certain command trait? Change one of the two slightly to fix that problem. Want to revisit an old faction with just a single new subfaction (like Legion of Grief)? Just print out a new card to add to the deck of LoN players.
Want to sell even more stuff: create lovely binder maps that allow players to only take the warscroll cards that are currently used in their army. It would also declutter a wargaming table (an epiphany I had recently by playing on a lovely table with 2 fully painted armies... But it was still a mess of cards/books/dice/... all strewn around the table).
Why do I not like only tweaking via points adjustments? Because it can ruin the entire feel of an army. I play Grey Knights in 40k... A supposedly elite force. The rules they gave them are so poor, that many of their units already dropped so massively in points, that they are actually losing that elite aspect of the army. I'm beginning to outnumber most typical marine armies and fielding "hordes" of low point power armoured Grey Knights is not what I had in mind when I started collecting the army (nor is how they are described in the lore...)