This is such a cool idea for a deck! I love the snake tokens, and -1/-1 counters have always held a special place in my heart (I'd like to thank Scars Block for that one). As you mentioned, it definitely could use some improvement, so I'd like to add my two cents (from a slightly competitive viewpoint, hope you don't mind). I know you're working off a limited card pool, so I totally understand some of the more unusual card choices.

"Problem 1: this deck does not take advantage of the Commander's abilities by spamming -1/-1 counters."
I agree. I'm seeing maybe two other cards that even make use of -1/-1 counters. The commander's abilities seem...alright, but not really for an EDH format (I don't know what legendaries you had to choose from, but this one seems really difficult to work around.) I'd add more -1/-1 effects into the deck to get those sweet sweet snakes. Also maybe some fear/intimidate effects so you can connect with the commander for more snakes.

"Problem 2: this deck doesn't really incorporate green's mana ramp or big beasties."
It doesn't and it absolutely needs to. EDH is a typically a slower format; you have time to get those fun, higher costed cards out; might as well throw some big spells in and shake up the table. Your mana curves out at like 2-3, you could definitely make room for some higher costing cards if you have them available (and if they're worth it).

"Problem 3: This deck doesn't focus on any of the swampy black mechanics to take control of the game."
Agreed. I noticed a huge lack of the board control, removal, card draw, and card advantage effects that black is known for. These would pair well with your commander needing to connect with your opponent for her to start getting snakey.

EDH is usually a multiplayer format that runs longer. You have time to get some bigger spells out. I'd throw some overcosted but cool effects in there if you have any. I would also replace the soft removal spells like Disfigure with hard removal. (And remove Illness in the Ranks, it kills your snakes.)

When I got into EDH I built my first deck out of my card collection, and the deck ended up being awful. You've clearly done a better job than I did, haha. I can't even imagine trying to make a deck with such a limited pool of cards to choose from. I always encourage people who are interested in EDH to go buy a precon. You're typically getting a well made deck wth good synergy, and getting some real bang for your buck. Then you can build forward from a good base.

Awesome post and deck, and I'm so glad to finally find a MTG community! (I'm game if anybody wants to sling some spells on untap.in or any other method!)