What to spend my runes on.

Yes, I do plan to donate to the guild by the thousand, once I have a solid card base. But until then? I plan to get one or two more 10x summons.
Should I increase hero limit/ card storage? My friend limit? Or are those kind of useless in the long run?

There's no need to donate runes to the guild. Save them and spend them on strengthening your team.

Slots and Storage are not something that everyone invests in but I find them hugely useful. Slots allow sustained Auto-fight farming for exp, fodder cards, puzzle pieces, initiative skill feeder cards, upgrade armour sets and so on. Storage allows you to hang on to many more cards that you will need or want to work on at a later date.

Friends spaces are only really important once you can't add all of the friends that you want with the slots that you have. There is an achievement for having 100 friends but it's hardly worth worrying about.

Best use of runes in my opinion is AP refresh. You want to get to higher level ASAP which in turn give you more options faster in the long run.