I've read up a bit on the captured HO-229 protoype. RAF pilots refused to test fly it because, although it looked cool it was in fact a design disaster (and the engines were pretty unreliable too).
For instance, (from what I've read) it had no internal bulkheads between the pilot and the engines, there was an oil pump directly behind the pilot, there was no cockpit floor (canvas cloth only) until the front wheel was pulled up. I guess this was why Gotha wanted to redesign it before it went into production.
I'm sure that if the Germans had more resources the design would have been much better - but they didn't and it wasn't.
Also, the broad flying wing design encounters severe aerodynamic problems when approaching subsonic speeds - particularly thick wing designs. This is why modern supersonic aircraft are long and thin, not short and broad. Can you imagine being the fastest fighter in the sky but knowing that if you go just slightly over speed you'll suddenly break up? Zoom'n'Boom would take on a different meaning.