I'm going to dump some suggestions in here (as a newly paying customer):
If I only have one domain, I'd prefer that it automatically expands on the dashboard, or remembers that I expanded it at least. I know there is a settings option for it, but it should be on by default for single domain accounts.
I'd like to be able to disable/hide/whatever the bing data. It's annoying as shit when it gets in the way on the graphs when you're trying to work out what the google position was above it and the bing thing is hovering where you want to be. Bing accounts for <1% of my traffic, they can go suck themselves.
The traffic estimates are incorrect as they don't take into account my geo preferences. If my site is .au, .uk, or whatever, I'd like that traffic estimate to be relevant to my needs.
There needs to be a bulk remove tool. I want to be able to select 10 keywords at a time and remove them all with only a single confirmation.
There needs to be a bulk export tool. I want to be able to select my 30 underperforming keywords, hit export, and have a list I can dump straight into another app without opening excel first.
If you put in a keyword accidentally that is 500+ characters long it breaks the layout.
When I add bulk keywords I can't see the full result due to the lightbox/modal/thing not being scrollable.
Showing 100 entries at a time isn't optimal. I'd prefer 200 or even better 500.
If I've added duplicate keywords, I'd like to know which ones they are rather than just a count.
Some > and < filtering by rank would be awesome, especially with bulk selection/export.
When you click the graph button it'd be nice to not lose your spot in the list when you're 80 keywords down. A modal or whatever would be great.