What base you build really depends on what is on the world and where, by default I would say any base would need to be no more than a couple hours from the star port. However if you have industry spread far and wide, I would recommend smaller bases near those assets.
Other than that, run with what works, Castles Brian.
As far as geography, mesas and mountain tops were great pre-airplane, after the invention of the airplane, there is really only one choice, underground, with hidden exits, self contained power, water, and waste recycling.
As far as defense, Hidden Turrets, Mix of LRM, Medium Laser, and AC/5. Once inside lots of Medium Lasers, Flamers for infantry, ability to flood portions of the base and then drain them. Your defense is mostly being hidden that is what matters. However that is still only going to work once, unless you take lots of time, making the hidden entrances and exits far from the actual base, even then eventually they will find you.
If you really want to have fun, a Giant Sub like the Wyrm that WOB used on earth. Took the Republic Years to hunt down, it moves, it can be big enough to house basically anything in numbers. You just have to make sure it is not so big, that it limits where you can take it, or how close you can get to shore. You don't really want to drop you mechs 100 miles out to sea and make them walk ashore. Post Jihad though there is the Tonbo, Air Cav for Mechs.