How bad is it to be second eleven?

"Second eleven" would never be used outside a sports context - except as a metaphor, in which case it is common. A school, or club, or other sporting organisation, will have a First Eleven in a sport, who are the best team they can field. They will also have a Second Eleven, who are just as keen but less skilled, and possibly a Third and Fourth Eleven. ('Eleven' has no mystic significance, but as it applies in football and cricket as well as other less-known sports, it is often used to generalise. The company's First Eleven would be the best employees they can provide in the field under discussion, who are as likely to be contract negotiators as the literal footballers; the company's First Fifteen in either England or France would probably be rugby players, which makes it a less understandable metaphor.)

So second eleven as an adjective means 'not up to the standards of the best available'. There may be a further nuance, in that the Second Eleven (in sports) is often where you find those who have mastered the physical skills necessary but not fully understood the tactics of the game, which would suit your context; but I wouldn't say that's widely applicable, let alone universally agreed.