...would think the organism that endured more time on the planet, became more complex (
I don't think that is what the ToE would predict. It may or may not. I don't think it's true either. There are just exceptions here or there where a later organism is more complex than an earlier.
I don't see any reason to expect a modern microbe to be more complex than an earlier one. At this point we would have to know what "complex" is.
If you mean a larger genome then I'd have to see number on the range of bacterial an archean genome sizes and try to guess from that if there has been any overall increase. I think it would have to be a guess since we don't have genomes for actual ancient microbes.
I also thought that bacteria were mostly pretty close to minimum genomes for what they do now but don't know much about it.
What goes? The Nose Knows!