If you are a clean slate and can't find a true MMA gym then I recommend Judo. I find when competing Judo is my fallback discipline. There are a LOT of wrestlers moving to MMA. When I match up with a wrestler I quickly learned not to play their game. When trying to wrestler with collegiate wresters I found if they wanted me down they could get me there. If they wanted back up, not much I could do to stop them. I quit trying to wrestle with them and started using some Judo sweeps of which they were unfamiliar and I could put them down without getting into a contest of strength.
Judo and wrestling is the transition game of MMA refined and either of these will give you a better chance of determining where the fight ends up. I would say Judo since it sounds as though you are more interested in submissions versus ground and pound.
A lot of fighters love Muay Thai and BJJ. With these disciplines you are competitive regardless of where the fight ends ups but you most likely will be competing at the weaker aspect of your game if you are fighting someone who controls transitions.
I honestly wouldn't recommend training at different locations as the whole is greater than the sum of the parts. Knowing how to put together the different aspects of fighting is what will make you successful.
Also, avoid a classic boxing gym. The transition to MMA requires a boxer to unlearn a lot of footwork an you will learn some very, very bad habits when it comes to blocking punches. Find a good MMA boxing coach. I equate a classic boxer trying to box in MMA at more of a disadvantage than a BJJ practicioner (Gi, no striking) would be in a Gi-less MMA fight.
Judo can also teach you intermediate submissions and submission defense. Judo can be in the same boat as BJJ, without a Gi is a whole different game and still needs to be adapted to MMA.