There's some good suggestions here, but also some less-than-good ones... I'll just go through them all.
-Lengthened campaign/story mode. It's great but it's too short.
I would have liked it to be longer too, but I was pleasantly surprised by how much content there actually was given than this is primarily an online game, and the single-player comes second. In any case, it's too late to fix this now.
-Greater customizability with gear. Let us choose colours and perhaps a way to transfer abilities between gear for ideal optimizations.
Random colours is good, it forces you to stay fresh. Preset weapon sets were a really smart move to preserve balance and prevent one combination steamrolling the rest.
-Bots. This can't be stressed enough. Even a single bot could have a dramatic effect upon the outcome of a match. We've seen how bad it is when just one person dc's from a match. They are completely one-sided.
Yes, this would be good.
-Spectatable matches. Really wondering why it isn't there.
This would be neat, even though there isn't much great strategic play worth spectating right now. I'm quietly expecting this to show up in August.
-Let players leave lobbies instead of forcing them to stay in the room or turn off the console.
Yes, good.
-Higher level cap. A day after release I already saw players at level 18.
This will absolutely 100% definitely happen in the future. It's low right now to stop players blasting through to level 50 or 100 or whatever, then never playing again. When the cap gets raised, players will come back to hit the new target.
-Red, black, and white ink.
Red looks like blood, and (from a colour theory perspective) just doesn't fit with the rest of the game's slightly kooky colours.
Black looks like oil, wouldn't fit at all with the other colours and would be really gross to play in.
White... You know what white ink looks like. ಠ_ಠ
-Get rid of the news 'update' from Callie and Marie. We don't constantly need to be reminded of what maps there are every 4 hours or every time we turn the game on, nor do we need to be kicked offline just for these updates.
I suspect this is unskippable for technical reasons, rather than because the devs just wanted to make sure you don't forget about the Squid Sisters. I can't say for sure, but it may be to cover the new maps being loaded, or to make sure everyone is synced to the new set of maps. Either way, I'd much rather see some cute squid idols than a loading bar.
-This is personal opinion, but buff the ink brush. Was really looking forward to that and was disappointed to see that it wasn't that great when I used it.
You don't have to look far on the site to find people declaring their love for the Inkbrush. It really is great when you learn how to use it. (Tip: its speed is its greatest strength - us it!)
-Make online matches more randomized. Many times I'll see all the higher level players on one team and all the lower levels on the other. Again, this mostly just leads to unfair matches that are pretty one-sided.
Sounds like confirmation bias to me. The teams really are randomised.
-Change loadouts between matches. This has self-explanatory benefits.
Yes, this would be good.
I could go on even longer about the "we need more squid hairstyles" thing but... maybe that needs its own thread.
