I like Syzyx's ideas. Making a graduated set of penalties adds a general cost instead of making all-or-nothing pockets for advanced technologies.
Personally, I'd dedicate X slots as superheavy slots, add a tonnage surcharge, and slap to-hit penalty on it with those additional crits.
Making superheavy slots means you don't need to designate internal/external and you get to use an existing system.
The tonnage surcharge would allow a graduated penalty for the number of slots instead of a flat -1 to-hit against the unit. Either a flat rate for the equipment, 0.5 tons for every 2 slots (or fraction of 2). Or a 10% bump in the 'mech's structure weight for every 2 slots (round up to the nearest half-ton) . That's 60% to turn one side torso into superheavy slots (reduced back to 30% with ES). For a Locust, that's +1.5 tons for 12 slots and for an Atlas, that's 6.0 tons for the same. Both get reduced by ES normally.
For an in-game effect, I like the idea of a defense penalty, but that -1 to-hit is broad. What about: For every N slots (or fraction of N slots) on the 'mech, 1 point of to-hit penalties for Terrain or Movement are ignored. If you're going to stand in plain cover, there's no penalty, really. But you're going to stick out of/above terrain and be a big blob no matter how fast you move. Granted, after 3N or 4N slots, there's really no penalty for assaults taking more. Maybe if we threw in Range penalties as well?