I just got this yesterday, I'm not really sure how to play without using the Phoenix units? Like Stage 2 of the MSG storyline, I have no idea how you'd have enough units to complete it just from playing Stage 1.
Are you playing the English version?
Stage 2 is actually considered one of the most grind-friendly.
First, don't rush enemies let them come to you.
Second, guest units (Guncannon, Guntank, Core Fighter) have higher stats than enemy units, so you can use them to trim down enemy numbers.
Then you hit what's left of enemy units with the guests and finish them off with your originals. At this point in the game you should already have access to the Zani, it's basically a Jim with an insane long range rifle: buy a couple.
Third, use squad attacks and master squad attacks (the manual should make things clear for you) and double tap every enemy (shoot everything using two units, not just one). Finish off the flying magellas with melee, otherwise you won't have enough accuracy to hit them.
Don't waste your time fighting the Dopps in the sky, they'll come to you.
Always check on enemy units' range, since most of them have blind spots.
My cousins are playing the game, they used an app called "Qooapp" from the play store and then downloaded Cross Omega. It seems there's no official way to play it outside Japan (Chile here)
Oh, too bad. Lucky for me I just saw the New Years special and the cringe sort of made me feel less hurt for not being able to play this thing. Wish we'd get an updated version of Supa Robo Gakuen on 3DS...