@BitBadger
I'm a new user, but I have used CoinTracking extensively. I thought I would give you my thoughts from the perspective of a user.

Re the real time API. It depends on how "real time" you want/need. CT will automatically import once a day. However, once you have set up the job, you can do this manually once an hour. (Enter Coins => Automatic API imports). If that's not often enough, that will need to be addressed by Dario/Kevin

Splitting trades by portfolio can be done (Enter Coins => Overview and Manual Imports), Once there, you must change to View:Extended (at the bottom of the table). I would also set Inline Editing:On  Set up that way, you should be able to see Groups and be able to click on a trade and assign it to a group to create the "sub-portfolios".  Done at this level, you could assign a transaction for BTC to one Trade Group and another BTC transaction to a different trade group, regardless of what Exchange it was done on. I recommend that you actually set up all this with the 100 trades that will be in CT once you set up all the Imports and Groups. For this test, you don't have to assign real groups just to test it out and one of your groups can be blank for this test (or later), so you don't have to put a lot of effort into checking out if this would work for you.

From my own experience, if you use CT, you will want to assign those groups as soon as the import is done because it could quickly get away from you as to what belongs where. It's also possible to export the entire table to Excel, add the Groups (you could assign multiple transactions this way) and then import the finished spreadsheet. This is where Bulk Delete would come in handy, because you would want to empty the table before you uploaded the revised spreadsheet, otherwise you would probably get double entries. If you take this approach, you would want to put API Imports on Manual so that when you empty the table it stays that way. You can also back up your table before doing any of this so it's easy to recover from any mistakes.

Once you have some groups assigned to some trades, you can view a report (Reporting => Balance by Exchange). At the top of the report, there is a button titled: Group by Trade-Group. This is referring back to the Groups you defined above. That probably isn't exactly what you want for a report, but you can see how it works. I think the report you would want is Reporting => Realized & Unrealized Gains. Unfortunately, that page is only displayable by currency right now. However, I'm guessing that Dario could add a couple of buttons to toggle back and forth between Currencies and Trade Groups. He might even be able to have the Groups report give the user Gains/Losses grouped by Trade Group, then by Currency.

So, my recommendation to you is to use your free access to test out these ideas to see if it will meet your needs and go from there.

I hope this helps.

Steve