Hey Ben!
I'm a newbie here at Riptide who just signed up to provide some feedback on Cubetutor. I've been using it pretty actively for several cubes in the last couple months and have recommended your site to several friends already. I do believe you're in the process of going viral, and I suspect your user information confirms that

First and foremost, I wanted to thank you for the incredible tool you've created here, as well as the openness you've been demonstrating through development so far! You have an excellent start on something here that could be a huge asset to your career if everything goes right. I know I'll be rooting for you!
I've come up with a short list of feature proposals that I'd like to submit for discussion:
-Re: cards in decklists subsequently deleted from the cube. Second the recommendation of others to partially move to a more generic id system that supports retaining deleted card info, BUT: Add highly visible text high on the page announcing that X cards in the deck have since been removed from the cube and optionally designate those cards in the list view (but not in the popup image) somehow (an icon on a corner of the card? shade the card heavily? overlay a large icon on the whole card image?)
-Cards at the bottom of the screen have unreadable popups, because the popup increases the page length and hides the bottom half of the card, but scrolling down to view the hidden section removes the popup and shortens the page again.
-When drafting, popups of cards seem unnecessary since you're displaying all the cards in visual format already. Could the draft view be rewritten with no card popups, and instead bringing the card currently under the mouse to the front? This would maintain the compactness of the view as well.
-A "See older posts" button for the Blog would be nice.
-A link to this forum should be somewhere accessible from everywhere on cubetutor.com, under "Feedback" or something similar.
-Seconding of course the many requests for edit/delete of Blog posts and saved Decklists, both by the
submitter and the
owner of the relevant deck or cube.
-Opt-in notification by email and a notification icon on the site (take inspiration from social media here) when someone other than you: saves a draft deck in your cube, comments on something you 'own,' replies to one of your comments
-At the end of a draft, at the deckbuilding screen, show a small diagram with the
position of the human drafter and the bots and the
colors that each bot was in. Optionally, allow clicking on a bot to open their draft pool for deckbuilding.
-In deckbuilding and with saved decks, add a new string to the deck breakdown for "Total Lands: X", either before or after the Basic Lands count.
-I've also been thinking about the correlation of cards issue for bot picks, as well as for player analysis. The amount of additional cloud service you're willing to pay for is a big question here, but maybe these ideas will excite you. From
saved decks only, track the frequency with which a card appears in conjunction with each other nonbasic land card, as well as the total # of land it appears with. Separate these statistics for the relevant cube and across all cubes. This information could then serve as a basis for a huge amount of user service and tweaking of bot pick orders. For example: bots consider curve and card coincidence rates when picking, or a "suggested card" section for cube lists that shows cards that appear in decks with cards you already have sorted by calculated coincidence rates, plus user-adjustable settings for price/format etc.
I'm sure I've already listed far more than enough, and I'm eager to hear feedback you may have. I would also second the recommendation of others to partner with some sort of online store for card links if you're looking to recoup some of the costs of the site and still keep it free and ad-free.
Thanks again for all the incredible work you've done so far!
EDIT: PS: wrote this wall of text while in the middle of a CubeTutor draft. Looks like UR tempo aggro!