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Is it not doing a good job?
I don't know - I imagine route planning is quite a tricky thing. But for example, I'd be curious to see how much the route would really deviate if it had a higher weighting to quiet roads. Same goes for avoiding hills etc. To my eye, the route goes very near some big national cycle routes. but doesn't opt for them. This may be because of the preference for paved roads, or just a random quirk.
I guess my point is that I can't visualise the selection criteria or reasoning behind some of the route choices.
Part of me would think that just following a national cycle route would make life a lot easier on a big solo ride for example.
Nef-
Assuming you're talking about the UK, the National Cycle Network is notoriously awful and full of mudbog footpaths, flights of stairs, soft sand beaches (!) etc because Sustrans favours "traffic free" over any sense of sanity.
https://twitter.com/hashtag/Sustransed?src=hashtag_click
So something being part of the NCN doesn't tell you anything useful about whether it's good to cycle on if you're trying to make progress.
grams
AFAIK that's exactly what that site does by default. Is it not doing a good job? You should contact the guy who runs it if so.
It does tend to send you through local parks / shared paths / etc in built-up areas, which won't do anything for your average speed.