Bill:
Superhuman Physical Characteristics - not really mattering on this level
Immortality (Types 1, 3, and 4) - Meh. Nothing she can't get past
Regenerationn (At least Low-Godly, possibly-Mid Godly, he spoke an ancient incantation before his demise that can allow him to come back from being erased) - not combat applicable. Homura isn't one to just let an enemy recite the AXOLTL.
Teleportation - she's Omnipresent
Mind Control - Homura has some of her own and can resist witches kiss, can resist Madoka's memory erasure wave - she'll probably be ok.
Reality Warping - useful as hers.
Inter-universal travel - She's omnipresent. But counters her BFR
Time Manipulation - she has some of her own to counter. Plus she's omnipresent throughout space-time, which tends to mess up all time shenanigans except the most wide-scale. Plus destruction of her physical form won't do anything to her.
Dream Manipulation and Nightmare Inducement - meh. She's lived through all her nightmares about 100 times.
Clairvoyance, Precognition and Cross-universal awareness (is capable of viewing different realities) - she's omnipresent throughout the multiverse's time-space. Everything he can see, she can also see because she's there for it.
Illusion Creation - on this level, kinda meh
Intangibility - on this level, very meh
Energy Projection - on this level, very meh
Flight/Levitation - she's omnipresent
Matter Manipulation - pretty sure WoG says she's a deity and her true form is non-corporeal just like Madoka, so... meh. Plus, destruction of her physical form can't kill her.
Possession - She'd probably eat his soul if he tried. Plus, again, resistance to witch's kiss.
Fire Manipulation - at this level, meh
Size Manipulation - she's omnipresent. Can't get much bigger than that.
Telekinesis, Telepathy - kinda meh on this level, but counters her's I guess
Madness Inducement (Can create bubbles that can induce madness into whatever it touches) - she's already kinda insane. I doubt it would do much more than annoy her.
Fourth Wall Awareness (Is aware of the real world and can "see" us) - unless he's seen Madoka Magica, not helpful. Hell, even if he has seen Madoka Magica it still isn't helpful because nothing in that show even hints at a clue as to how you kill Homura now that her Soul Gem is destroyed.
Soul Removal (Did this when he possessed Dippers body) - she doesn't have a soul to remove. Maybe he could possess her body because its already soulless, but that body isn't really important to her anyway.
Resistance to reality warping and space-time manipulation - took out time baby, but Time Baby was only low 2-C, while Homura is 2-A.
possible Higher-Dimensional Manipulation - 2-A lowball so ignoring.
Homura (Don't know how much of her magical girl and witch stuff she keeps, so I'll go over it all) Superhuman Physical Characteristics - not really mattering here
Firearm and Missiles Mastery, - kinda meh on this level
Time Manipulation. Time Stop, Time Travel - helps her counter his
Technological Manipulation - kinda meh on this level
Immortality (Type 2 and 6 [Though the latter should not come up in combat.]) - so she can keep fighting even with injuries I guess.
Forcefield Creation - maybe? Helps against energy project I suppose.
Weapon Creation - kinda meh on this level. Maybe she can make some magic shields or something
Mind Manipulation and Magic Resistance - only resisted witches though iirc. And they aren't close to Bill's level. Maybe keeping her mind despite Madoka's universal reset is a feat?
Healing - so she can fix herself up if he damages her.
Telepathy, Telekinesis - kinda meh on this level, but counters his I guess
Transformation Power Drain - no clue what this means.
Magic Sensor - she's omnipresent, so kinda redundant.
Weapon Enhancement - kinda meh on this level
BFR (Through sending people to her shield's Pocket Universe) - Bill's interversal travel counters.
Time Paradox Resistance (Through contact with her shield) - acausal now, so redundant. Could help against his time powers though, if her other stuff doesn't already.
Energy Projection - kinda meh on this level
Memory Manipulation - he has no resistance. Plus, that's kinda what took him down in the end.
Transformation - meh
Familiar Summoning - witch's familiars are fodder to BIll
Reality Manipulation -useful as his.
Pocket Reality Manipulation - she probably has it technically, but she can also control normal reality so...
Soul Manipulation Immunity - counters his soul manip
Acausality (Only on 3-D scale) - stops him from affecting her with normal time manipulation. Not sure if he can control higher dimensional time, which is what he would need to affect her.
Concept Manipulation - he has no resistance, she can crush his concept.
Dimensional Manipulation - Spatial manip? He resists, although apparently only against Time Baby
All in all, giving it to Homura. She has more consistent counters and resistances to what he has, a few abilities of her own that he doesn't resist, and also has better feats compared to his lowball ("a threat to the multiverse" vs "taking down a multiversal being"). Plus her personality is better suited to fighting. Bill plays around. She doesn't