If MergeMetaTriangles takes a long time, check if you have any large liquid surfaces such as slime/lava/water. These shaders usually use a high q3map_tessSize value and this causes the compiler to split up these shader surfaces into many triangles more than normal, and once MergeMetaTriangles comes around it causes it to work very hard and long to merge them into one surface.
Check your shader for a q3map_tessSize value. If the surface in GtkRadiant is very big(for example I did a very large "oceanside" part of my map with a really big water shader once and had your problem), try reducing the q3map_tessSize or removing it altogether. With a large brush, wave effects shouldn't be a problem(q3map_tessSize gives the game more triangles to work with in deformVertexes modes resulting in better looking waves for smaller liquid brushes), in fact it'll probably look better since a larger body of water tends to have larger waves.
This is just one way to fix it. It usually involves merging a lot of triangles so check if you have anything with a lot of triangles right next to each other(csg subtract?).
