Fuji says Niou isn't even close to the real Tezuka here:
http://www.mangahere.com/manga/prince_of_tennis/c363/13.html
Assuming he isn't lying or just playing mind games we'll have to assume this statement is readily obvious. Sanada described Niou's performance as 'clowning around', so certainly Niou overall performance is nowhere near Tezuka tier.
Sanada and Yukimura generally has shown unbelieveable knowledge about tennis, including knowing about Tezuka's techs that nobody in their own school knows about. Therefore anything Fuji can deduce, surely Yukimura can deduce if he actually played Niou. Since Yukimura didn't underestimate Fuji, unless Yukimura's well-known ability to magically know how good everyone he never played is suddenly fails him here, he should've seen some warning signs of this matchup. Given Niou needs some time to even get his illusion working, we'd have to assume if he did have a scrimmage of any kind against Yukimura he'd do even worse compared to how well he did in Nationals. So either they never had a scrimmage or Niou told him his illusion will improve by the time the actual game comes around.
Either way since Yukimura acts as the coach of the team, he is responsible for taking a gamble on an unproven player. The fact that anyone else might've still lost to Fuji is irrelevent. I highly doubt Sanada would describe Yanagi's performance as 'clowning around', so at least expectation-wise, Yanagi is certainly regarded as a better player than Niou with illusion.
Sanada got the Emperor title for crushing people head-on and he abandoned it, at Yukimura's request, to beat Tezuka. We'll ignore whether that scene even makes any sense but that's the sacrifice Sanada allegedly made for the team.
Sanada absolutely isn't going to go cry to Yukimura that since he lost to a kid before Yukimura must avenge him. Sanada obviously understands that winning is still more important than his pride, which is why he agreed to Yukimura's advice in the first place, so there's no argument about Yukimura attempting to 'avenge' for Sanada. That also goes directly against what he preached about winning is the only thing that matters.
Yukimura purposely waiting for Ryoma is not unlike Ochi giving the tiebreaker to Atobe/Niou when Kabaji jumped in (the point should be replayed and under no circumstance should Atobe/Niou team get the point for using 3 guys to score). There's nothing honorable or noble about such an act. It's just plain stupidity. It's not like Yukimura sent an assassin to knock out Ryoma and then later decided that was dishonorable so he got to wait. You're not obliged to do any more than what the rule says. Honorable means you don't just say "Quick disqualify that guy before he gets here!" Had the ref asked Yukimura if he was willing to wait a few minutes, the honorable thing to do is agree to the ref's request. But that's not what happened. Yukimura participated in a circus act from Kintaro that's clearly designed to keep the ref distracted so Ryoma can get there on time. Although he talks about how winning is all that matters (which is why he scoffs at the concept of TnK requiring you to enjoy tennis), he put his pride ahead of his philosophy and that cost his team the championship.
---------- Post added at 10:48 AM ---------- Previous post was at 10:37 AM ----------
One piece of key information that's missing is how long did it take Yukimura to play Kintaro. Kintaro asked for just one point, but we know 'one point' can last a very long time in POT. I don't think it's a case where Yukimura played Kintaro for less than 5 minutes, beat him, and then Ryoma arrived, because you'd think the ref is willing to give 5 minutes for people to show up. So I assume based on that scene Yukimura took a nontrivial amount of time to deal with Kintaro, simply because Ryoma needed that much time to get his memory back.
Now, if POT is so hardcore that if you're not present at the time the match begins you automatically forfeit, no question asked, then that is just Ryoma's fault for not being there on time in such a harsh environment.
Note that Inui had to forfeit a game in U17 due to a stomach problem and his opponent sure didn't wait for him.