Played Enemy Within, and remembered that Apocalypse has something similar with Hybrids and Androids and the background fluff about modifications. Since the chances of OpenApoc becoming a reality are slim at best, here are some suggestions for augmentations for post-1.0 UFO and TFTD:
Basically a modified version of Genesis/MegaDrive Shadowrun system, your soldiers start with, say, 100 points of unmodifed flesh distributed over the body (50 Body, 20 Legs, 20 Arms, and 10 Head) and you can spend them on cybermods and genemods, both with their own pros and cons. Both of them can be taken at the same time, but are not very compatible: Each cybermod installed increases the costs of installing genemods and vice versa.
Alternatively, there are no limits, but each mod slightly increases the installing price of the next one of the same type, and greatly increases the costs of next one of the opposite type.
Other suggestions:
1) Original Deus Ex-like slots, with certain mods only allowed in certain slots.
2) Limited number of universal slots.
3) Unlimited number of universal slots.
Other limits:
1) Upkeep in money, special materials (ala Meld) or both;
2a) Past the certain threshold, the Soldier may suffer side-effects that range from merely annoying to fatal. Ex: All mods the Soldier has on him/her have a total value of 80 points, right at the threshold of 80 points, but if more mods will be added than his/her organism will become unstable, at which point the soldier will suffer penalties or outright die;
2b) Past the certain threshold, the upkeep costs increase dramatically;
2c) Some mods, events and injuries can decrease the Threshold.
2d) You cannot cross the threshold.
EDIT: Costs, upkeep and thresholds can be altered through research.