Crono, SKIP brushes are totally useless unless one (and only one) face of the brush is textured with HINT. The reason the texture is called SKIP is that it says to the engine, "Ignore me completely". I expect you meant CLIP brush instead.
WD, there is a very easy solution to your MAX_MAP_CLIPNODES problem. To understand how it works you must understand what clipnodes are. Clipnodes are like an invisible shell (hull) that stops players, monsters and items from falling out the level. Without a clipping hull, the map world would not be "solid". The clipnodes determine where you can go.
Normally the clipping hull matches almost exactly with the visible hull (that is, with the visible walls and ceilings). The more complex the walls and other solids are, the more clipnodes need to be used to create the clipping hull (it's like making a picture from join-the-dots, but in 3D). There is a limit to clipnodes, which you have hit.
However, you can simplify the clipping hull without changing the visible hull. For example, cover one of your jet planes with a box. Texture this box completely with the CLIP texture. Now when you play the map, you will find that there is an invisible wall around the plane. The benefit you get from this is that a box shape uses 8 clipnodes (I guess), whereas a complex fighter plane uses many hundreds or even thousands.
[addsig]