Hi Rooze,
I know swarms and more subs are the popular thing, but I dono't think that's the first direction.
I have a Hsu and I love it, but integration is key. The issues you have described may not be phase related at all.
Do you have any bass traps? Consider adding those to your room. Talk to GIK Acoustics.
Yes, JL audio's room EQ is awesome, but also, you can do the same with your current subs and a miniDSP HD unit. Either will, with the help of bass traps, fix your issues. The problem is the learning and implementation. If you have the money, and don't want to go down a rabbit hole, get the JL subs. If you have the time, and want to learn, miniDSP with Room EQ Wizard is your most cost effective and just as good solution.
I mean it when I say this, JL Audio won't be a better sounding solution than what you have now, but it sure will be faster. :)