Altera CE or Arjuna CE? [Event]

Arjuna CE, absolutely. The anti-Divine bonus it has is extremely useful in the future and it's basically the only CE that gives it for the entire battle.

If you setup your bonus drops properly, I don't see why you couldn't MLB both.

This is a really long event, you have 2 weeks.
If you don't waste coins on those useless chocolate CEs you should be able to MLB both CE and at least get closer to clear the shop. Just wait until the last day to use apples.

Both of these are good, but mostly just for challenge quests where you will find both divine enemies and enemies that spam evade or invincibility. At least get one of each, but if you're afraid of running out of farming time, probably focus on arunja because two effects get increased at mlb rather than just one.