Weakness - Generic stat-boosting option, same as last time. What you see is what you get, can't really go wrong with this. Not exactly massive gains, if the 2 points from before were any indication, but nothing to lose either.
Uncertain Friends Allies: Local - Of all the Allies options, this is probably the lowest risk. Mainly because - unless Mami's personality is significantly different from canon - the girl has a sense of honor and is unlikely to attack Homura, if all Homura wants is to do chat. Not even if she's highly alarmed about Homura knowing her civilian identity and where she lives. There's no guarantee she'll agree to anything, but also not much risk she'll try to take advantage of Homura later even if they don't come to an immediate agreement.
Uncertain Friends Allies: Distant - Slightly riskier. Kyoko probably still has her hypnosis (I think in canon she was using it to constantly book herself into hotel rooms) and might get alarmed enough at Homura knowing who she is out of costume to attack her. With all the parahuman gangs around, she might not trust that Homura isn't working for one of them. There's not even any guarantee Kyoko herself isn't in a gang, though if her personality remains intact, she's probably still a lone-wolf.
Unknown Actors - My guess is that this potentially includes Nagisa Momoe. But otherwise, it's a complete question mark. Unknown risk, unknown reward. Could include characters from Worm too, though there weren't exactly many known to still be in Japan, maybe the remaining members of the Sentai Elite previously mentioned.
An Unthinkable Alliance - The riskiest Allies option. Though probably also the highest reward if it works out, since unless something has dramatically changed, succeeding means a 2-for-1 deal getting both Oriko and Kirika. Oriko probably still has some kind of Thinker power, given her canon wish involved her wanting to know things. However, I have a suspicion Kirika's isn't going to be quite the same - her canon wish was to change herself for Mikuni, which practically screams having a Changer power of some kind. There's no guarantee that Oriko's power won't still feed her information to set her against Madoka and Homura, though if the Worm precog limitations about Trigger Events apply, there's also a distinct chance it wouldn't have. Equal likelihood of either happening.
Introduction: A Warning - IMO, this is asking for trouble. Madoka just lost family to parahumans, Homura coming by to warn her about more trouble could easily make her assume (correctly) that Homura is involved with parahumans and the trouble is another external parahuman threat. Which isn't precisely wrong when it comes to Walpurgisnacht, but the real threat is Madoka herself having a bad Trigger Event. Which putting stress and pressure onto Madoka could potentially accelerate, if it hasn't already happened.
Introduction: Normal? - The more sane option, IMO. Between the two introduction options, this would be the one I pick. If Homura still has the cat, it might be possible to leverage that to get in with her. Even if she botches it, that's probably less bad than trying to warn Madoka about threats when she's already been exposed to the dangers of superpowered crazy people.
Explosive production - This is like Weakness in terms of risk and gain, except we're getting a limited supply of bombs rather than a bit more muscle.
Supply Procurement - Like Explosive Production, except instead of bombs, it's for vehicles and other non-combat related tools. IMO, of all the "no-risk improvement" option, this might be the most useful. A vehicle would drastically increase what Homura can do with her limited few minutes of timestop. You can travel a lot further in a few minutes with a bike or a car than running.
Going Out in Disguise - The only real benefits of this is to build up a reputation and to get away with brandishing guns out in the open, since Homura's power isn't one that can visibly be seen as long as she doesn't get caught "teleporting". Unless we have a plan that requires Homura to have a big reputation or that requires her to openly go guns blazing in front of many people, I don't actually think Homura extensively benefits from a costume. At least not at this point - we don't even have any good guns to start waging open warfare with.
Raid the Roses: Part 1 - Out of all the "Attack" options, it's either this or the Church that are the riskiest options. These guys are brazen, they do home invasions and bombings and would probably start a gunfight on an open street if they thought they'd win. If we started down on this, we'd probably end up having to ally with people the Rose Garden already are at war with, which is probably going to be another parahuman gang, to get enough firepower to win. And then it's going to get messier and messier from there.
Hamper the Hackers: Part 1 - Pro: They have tinkertech to steal. Con: They have tinkertech to use on Homura. Though if forced to pick between this, the Church and the Rose Garden, I would probably go with this one as it seems the least risky of the three, due to them being less organized than the Church or the Rose Garden.
Contest the Cult: Part 1 - The description makes it seem like they've got a Master working for them. That sounds like trouble no matter what. On one hand, they appear to have Tinkertech knives to steal, but on the other hand.... the Master. Depending on how their power works, it could be worse than Rose Garden, since even though the latter are brutal and violence, they at least seem straightforward in their tactics. It could also end up being easier, if breaking the Master means that all the followers instantly stop following the Church (which is nowhere near guaranteed to happen).
A City of Danger - Out of all the Attack options, this one seems the least risky, as it basically involves only low-level criminals- though chances are at least one of the serial killers is a parahuman. This is also probably the option that is most likely to lead Homura to start her own parahuman gang.
Acquiring weapons: Military - This is probably not exactly a "no-risk improvement" option like Weakness or Supply Procurement since it runs the risk of attracting attention from the Japanese version of the PRT, but would likely require a critical failure for Homura to get any blowback from attempting.