I gotta say I enjoyed Progressive more between the two, it had a lot more going on like the original FLCL and did a lot to combine the "everyday" side with the crazy side like the original show. I found it more interesting.
Though I missed the more playful Haruko (like she's back as in Alternative) due to the split, though she's still good, but at the same time I totally loved Jinyu.
However, Alternative has captured the "everyday" scenes half of FLCL better than Progressive did, since in addition to having a lot more of it in Alternative we also surprisingly didn't really get to know Hidomi as much as I expected in Progressive since she was so bottled up. Maybe combine the two shows lol.