I like the Binding of Isaac/Zelda concept of dungeons mixed with the push-your-luck mechanic of creating your own dungeon (with more enemies - meaning more loot and many more occasions to get hurt).
The "connections" as a weapon is a fine concept, but I often struggled a bit when enemies where everywhere (especially in the corners, they really like those corners, huh?), also makes the screen a bit unreadable with all those projectiles and bright colors everywhere.
Chests and upgrades provide a nice progression system.
An obvious critique would be to mention the lack variety but I believe that you already know that and also it's incredible how much you put in this game in just 48 hours.
That is definitely something I'd like to see being developed further. I don't know if you plan on creating a bigger game out of this. IMHO, you should ;)