Just to go into nauseating detail...
Conceptual design of a new aircraft is basically a series of trade studies. You start with a payload, a range, a cruise speed, and a required runway performance, etc. That eventually gives you, based largely on historical trends, such things as weights, fuel requirements, wing areas, etc.
Once you have an estimated empty weight for the aircraft and some modicum of aerodynamic data for the various proposed configurations, you can start to trade off.
Gear doors add weight. If you just take off, fly around the pattern, and land again, it costs you more fuel to haul that weight around than the fuel it saves aerodynamically. At some set distance you can assume for the length of a typical trip for the proposed aircraft, the (small) aerodynamic cleanup of the doors will save more fuel than it costs to haul the weight of the doors.
Beyond that trip length, eventually you might save enough fuel (Assuming a given fuel price) to overcome not just the weight of the inner gear doors, but also the up-front purchase-price difference of developing and building the doors, as well as the extra maintenance costs they incur. If the aircraft is planned to fly farther than that distance more often than not, you put on gear doors. If not, you don't.
That same type of trade is applied to most design decisions on the aircraft, sometimes returning to decisions you've already made to see if a design change impacts the trade study for another design decision.
This is the reason you see winglet retrofits on 737's. With an increase in fuel cost, aerodynamic cleanup becomes proportionally less expensive. Eventually, the aerodynamic cleanup (Particularly on longer trips) pays for itself and turns a profit. At the fuel prices expected when the aircraft was designed, it wasn't thought it would pay off, but it will now.
Of course, sometimes a very small performance or cost penalty will be accepted for marketing reasons (OEM winglets sometimes being one of these cases). However, if you told the board of a major airline that they should buy your airplane because it has inner main gear doors, you'd probably be laughed out of the office, so they tend to succumb to the black-and-white, rational trade-study analysis more often than not.
Finally, if you can't justify the time and expense of a trade study or if a good estimate of weight or aerodynamics can not be made, the decision might be made based on what the engineers like, what management likes, what looks like it might work best, or what's easiest to do.
As for the Nitrogen-filled tires, I understand some of the reason to be that Nitrogen is not flammable.