Based on your explanation, I'd venture to say it is the technique, not the equipment.
Actually, even without your explanation, I would again say the same. Why? Because for the vast majority of photographers (myself included) contemporary equipment is much better than their (our) technique.
There can not possibly be anything wrong with the 50/1.8, under normal circumstances (if there is, it should be sent for repair). It is a highly esteemed lens, with excellent test results (its MTF chart is even slightly better than of the 50/1.4), generally considered one of the best value-for-money lenses there is.
Also, I am a bit perplexed with your claim that for 100/2.0
the results are much crisper and better colours - but the longer lens is very inconvenient.
If anything, results for the 100 should be softer, given that hand shake would kick in sooner (approximately already below 1/160s, vs. 1/80s for the 50). There is no reason for the two lenses to differ in color either.
And how is the 100 "very" inconvenient? It would be only about 50 % longer and heavier than 50/1/4… sound a lot in percentages, but really not so much in real life, as both lenses are relatively quite small, especially compared to today's ubiquitous zooms.
As for the flash, you just said "no flash". Is it because flash is forbidden there, or you do not want to use it, and if so, why not?