While the typical definition of any class-based game is to have multiple classes that have varying and differing strengths and weaknesses, I feel that the current class penalties for the three lockdown classes are so ineffective as they are in tier 3 that we may as well get rid of them altogether.
My reasoning:
--Strikers--
~ Health Penalty: 3 pips of health is inconsequential and easily over-compensated by heart pendants. In fact, all this really does is make it harder for newer or less-rich players who have not yet built a pair of pentas to compete with other, wealthier opponents. In essence, it creates a case of "Haves" vs. "Have-Nots". Three more pips of health on top of 21 on a striker with two penta-heart pendants is not going to make any noticeable difference anyways, so to remove this penalty would only truly benefit the "have-nots" in this scenario, and even then, not in a way that would make them significantly stronger.
~ Bomb Charge Increase: The mechanics of the striker class itself is already unfriendly to bombers - how many striker/bomber loadouts have you ever seen? I've perhaps noticed two so far, and neither were remarkable enough to make me say "Boy, good thing that CTR debuff is there, or else I'd really be in trouble!" All this seems to do is just shorten an already small list of niches for bombers in PvP outside of mist-bombing. Even if bombers really wanted to bomb with this class, there are so many ways to get CTR buffs through gear, weapons, and UVs that it's not even that hard to get around the penalty anyways. I mean, even without this penalty I don't think the few PvP bombers left in this game are going to have a mass exodus to the striker class anyways, so it feels also rather unnecessary. It's like verbally and physically threatening a group hemophiliacs not to swim in a lake filled with leaches and broken glass - I don't think they were going to bother anyways.
--Guardians--
~ Gun ASI Low Penalty: Rather useless. All the serious gunners seem to go striker, and all the new gunners go recon. Like the above with striker/bombers, while I can see some gunners make use out of this class, this penalty is so inconsequential that if any of them wanted to do it, they would have simply already done it.
--Recons--
~Sword ASI Low penalty: Inconsequential. I know this for a fact, because I personally favor going as a recon/swordie and the Sword ASI penalty is not even noticeable. ASI is easy to come across and compensate for, as well as the mechanics of the class favoring well-timed tactical hits instead of mashing the first swing like a striker.
~ MSI Low Penalty: People hardly even notice the ASI Med bonus on mercurial gear, and this is barely even as noticeable as that. While it does make it harder to to catch up with the occasional running coward, the fact that almost everyone chooses striker and thus has a strike booster makes it already impossible to catch runners or outmaneuver the still-living ones.
Conclusion:
The point of this post was to question whether any of these penalties did anything to help the game at all. I find them all negligible or redundant and therefore think that it would only make T3 PvP better by making the class metagame more interesting and open to different class/gear combinations. Most, if not all of these "penalties" are so arbitrary and pointless, that even if they were removed, I don't think they would change up lockdown to the point of any noticeable significance. My thoughts here are more along the lines of "Oh, why the Hell not?". It's not going to change anything, except to perhaps limit some minor annoyances.
If the penalties are negligible, then perhaps they shouldn't be removed, but increased. Make the Health penalty a percentage rather than a straight 3 hearts. Increase the other debuffs to Medium instead of Low.
I'm not saying that should happen either, but it makes more sense than what you're suggesting. If they truly are unnoticeable, then why bother removing them?