The Mega Finale's branching Timed Research asks you to choose Chespin, Fennekin or Froakie. Scopely's own page says the choice decides which GO Pass rewards you get and "which Kalos first partner Pokémon Mega Evolution rewards you'll work toward", so you're really picking one of three Megas. Here is what each one does.

The short answer

Fennekin. Mega Delphox hits hardest of the three, by a clear margin, and Fire is one of the types you reach for most often in raids. Froakie is the pick if you already have Fire covered, because Mega Greninja is a strong Water attacker and a rare Dark one. Chespin is last on damage and no Grass raid needs it.

All three, measured

Damage per second at level 40 with a perfect attack stat, against a neutral target, using the Mega form's own stat line from the game's data files. Same method as the tier list.

What the choice does not change

The event runs the same either way, and nothing about the choice is permanent beyond the research line itself. If you only care about the avatar item, pick the one you like.

Event details come from the official Mega Finale page. The Megas' numbers are ours, computed from the game's data. See the Mega Evolution guide for how Megas work, or the calendar for what else is running.

Questions people ask

Which Mega Finale path should I pick?

Fennekin. Mega Delphox does 19.5 DPS, 5% more than the next best of the three, and Fire is a type you reach for often in raids. Take Froakie instead if your Fire attackers are already built: Mega Greninja is a strong Water attacker and a rare Dark one.

What does the Mega Finale choice actually change?

Scopely's own event page says it decides which GO Pass: Mega Finale rewards you get and “which Kalos first partner Pokémon Mega Evolution rewards you'll work toward”. So you are choosing between three Megas.

Chespin, Fennekin or Froakie: which is strongest?

Measured at level 40 with a perfect attack stat against a neutral target: Mega Delphox 19.5 DPS, Mega Greninja 18.6 DPS, Mega Chesnaught 15.7 DPS. The full table with stat lines and movesets is on this page.

Is the Mega Finale choice permanent?

Nothing about it is permanent beyond the research line itself. The event runs the same either way, so if you only want the avatar item, pick the one you like.

When does the Mega Finale run?

Whatever the official post says. Its dates and every other event's are on the calendar, taken from the post rather than from a schedule anyone assumed.