4. The colony building counts as an adjacent building for all other types of building. It has manufacturing, research, food, morale, and economy attributes and should be counted as a level 1 of each of those types for adjacency purposes.
Initial colonies already provide +1 level to any adjacent building, so consider this part of your request granted. I agree that 3 and 5 should be there as well, if we're not going to guarantee that the initial colony only spawns on a tile which is never adjacent to anything and never has a bonus. 2 is fine by me, as well. I don't know that I'd consider the initial colony a 'huge asset' if 2, 3, and 5 were added; at only +1 level to adjacent structures it's no better than any other structure for a highly specialized planet build, and depending on just how the level bonuses it would get from 5 work out, it could be a slight liability in a specialized cluster by reducing the total bonus from levels added to the specialty multiplier. On the other hand, it would in general be an asset for mixed and balanced planet builds.
Option 1 seems like the only decent alternative to option 2 or the combination of options 3, 4, and 5; if options 3 and 5 are implemented, then 1 and 2 are unnecessary, though the implementation of 2 would be appreciated, and I don't see much point in having only one or two of options 3, 4, and 5 implemented; with those three, I tend to feel that it should be all of it or none of it.
I found that what sucked in GC2 was conquering another race's planet only to find that the AI had placed tile developments inappropriately on tiles with an otherwise useful bonus, for example finding a research facility on a quadruple manufacturing bonus tile or, even worse, finding the starport built on a tile with any tile-bonus.
Absolute worst is the Hyperion Matrix on any kind of food bonus tile (especially the 300% ones), built on the Thalan homeworld. You can't get rid of it, and it boosts the population cap so astronomically that there's no reasonable way to control the approval rating of the planet. But yes, some work on the improvement-placement portion of the routines would be appreciated, especially since improvements and tile bonuses on adjacent tiles now matter when building things, in addition to what's on the tile you're improving.
But what if (unlikely I know) all the available tiles are bonus tiles? Maybe the player should be able to choose where to put the initial settlement, with an option for automatic placement
I actually don't know that this is terribly unlikely anymore, as Mountainous, Arid, and Grasslands tiles each carry a tile bonus before you add any special resources, and I'm fairly certain that I've seen planets where half or more of the tiles available were one of those three types (Mountainous and Grasslands are a pain to find, though, since they display no differently than the default prairie tiles).