ok, the main issue with the change of design is to tie in with the alien life cycle. All aliens with plain domed heads are classed as drones, think of them as teenage aliens if you will, as they get older, the domed head begins to shrink and fit tightly around the xenomorph skull revealing the indented head of the alien underneath, this is now what we commonly refer to as a 'warrior' alien, or a matured xenomorph.
Now in regards to alien 3 - the alien had crossed DNA mix with an OX so in physical appearance and movement slightly differed from those aliens who birth from human hosts. In essence, this alien is still a drone but with mixed genes taken from an animal. Som refer to this alien as a runner, but that is just a fabrication made up for the games and has nothing to do with the movies.
Scientific intervention and tampering was the result of the aliens we see in Resurrection, they are not average alien drones and were given a helping hand in their creation by scientitst working on the USSM Auriga. Geneticly tampered DNA crossing led an overfow of human genes being passed down onto the aliens making their appearance alter slightly and their intelligence level raised more than normal.
AVP - the aliens are just standard drones, nothing more, nothing less, though strangely their appearance is very close to the aliens from resurrection minus the different skin pigmentation, in instances like this i beleive it's just the directors personal preference on how he would like the aliens to look for that particular movie. To be technical, they should have looked like gigers drones, but as with technology, we have to move with the times and expect the special effects and puppeteering departments to progress and advance as time goes on.
Phew, hope i covered most of it.
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