If Barry Allen took their lives and shunted them off into the Speed Force, I can imagine they’d be a wee bit pissed off at him, and it suits the current MO Alchemy has, in restoring to people the abilities they had in a former timeline. He had his life stolen, so he’s giving back to others what was stolen from them and co-opting them into his revenge schemes.

I think it actually is Cisco himself:

– Cisco (and Reverb) can see through other timelines/realities rather easily.

– Cisco has seemingly learnt how to master his powers even more and let’s not forget what Reverb told Cisco last season “You don’t even know how powerful you are.” Being able to alter one reality using elements from another could be in that character’s possible skills (maybe it all started with him wanting to have Dante back from another reality to his, since Barry refused to help him).

– As you mentionned, the Barry / Cisco thing is a Chekhov’s Gun and Cisco doesn’t feel like he’s Cisco anymore. Grief is one thing but it also feels like it could be something else.

– Cisco being afraid to go to the darkside but Barry told him he’d be there to prevent that from happening, Cisco is blaming Barry for not being there.

– Dr Alchemy is not the only big bad of the season and this issue is probably going to be resolved before Savitar enters the scene. When there’s 2 villains in a season, if not in cohort, one is often a lesser villain or a misleading one or one causing the main one to appear like the Troika in Buffy playing the faux big bad of season 6 only to cause Dark Willow to reveal herself as the real one.

– Dr Alchemy didn’t feel that tall (though it doesn’t really matter since it’s likely a different actor under the mask for now).

– The overall colorimetry and lighting on the show this season on the Flash, in this timeline, is very oppressing, dark and gloomy (Barry’s lab and Star Labs in particular, in contrast with episode 1 in Flashpoint), maybe setting the stage for such a downer confrontation between these two friends. Last season they used such color filters to differenciate Earth 1 from Earth 2 giving the latter a more yellowish/sepia tint.

– Dr Alchemy seems to only be interested in giving people back what has been taken away from them from another reality (his brother has been taken away from him).

– Julian is way too obvious for now to be Dr Alchemy as such it’s probably not him, maybe he’ll turn out to be Savitar.

Personally I think it’ll end up being someone closer to Barry, but that idea would be GREAT.

If this is a Grodd setup I’d be cool with that — I gotta imagine he’s hard to write for on this show