Not to obsess too much over a rejection letter, but...
I queried the Senior Editor, received a request for the full from same senior editor, but the rejection letter came from the Editorial Assistant. The rejection letter was your basic "does not suit our current needs." The last line read, "And should you feel you have a manuscript suitable for X Books in the future, I strongly hope you'll feel free to query me again."
I figured that was basic politeness, but one of my writing friends insists that's a positive note meaning I don't suck and that she really wants to see something else from me. What do you think? Common courtesy or invitation? And, does it mean I should query directly to the Editorial Assistant instead of the Senior Editor listed on the website as the contact?
Your friend is right. If you sucked you'd have gotten a rejection letter with no hint whatsoever that you should ever contact them again.
Don't query the editorial assistant though. First of all, s/he's the assistant to the editor you queried most likely, which is why you heard from her. Second, editorial assistants move around like water drops on a hot frying pan. If they're good, they move up. If they discover they hate publishing, they leave. What that means to you is you'd be sending a query to someone not there, and if enough time has passed, no one remembers. Not a good place for a query.
If it makes you feel better, I get rejection letters from editorial assistants too, even when I've spoken to the editors about a project. I call em up and introduce myself of course but that's only cause I'll be talking to them once a month until they leave and it's always nice to know who they are.
Bottom line: keep writing. You're on the right path. And pay attention to your friend's advice about the stock market too.