It's a common thing...
Altering relative ages isn't new in superhero stories, they're just doing it a lot more often on this show. For example, sometimes Superman is older than Batman (he's often the original superhero), usually they're peers, and sometimes (like in the BvS movie) Batman is substantially older.
Few comic book characters have fixed ages, and the needs of any given story will generally outweigh whatever minor traditions have developed. In Batman Forever, Edward Nygma works for Bruce Wayne and seems somewhat younger than him, while in other stories they seem more like peers. It's just up to the writer, and what they think would serve the story best.
...and it won't matter as much when Bruce gets older
All of Batman's love interests on Gotham (such as Selina and Ivy) are around his age, and the difference between young Bruce and older villains will naturally diminish as he gets older.
For example, Cory Michael Smith (who plays Edward Nygma aka the Riddler) is currently 28, meaning the character could be, say, 26-30. That makes him 14-18 years older than 12-year-old Bruce. That's a lot older for a kid, but imagine the difference by the time he became Batman. Would you have a problem with a 20-year-old newly-minted Batman fighting a 34-year-old Riddler? Probably not. Frank Gorshin and Jim Carrey were both 33 when they played The Riddler.
Even a 30-year-old Batman fighting a 44-year-old Riddler wouldn't be that weird. He's not a brute-force fighter, so a Riddler with some grey at his temples might be kind of cool. Alan Rickman was 42 when he played the genius-villain Hans Gruber in Die Hard.
Yeah, Zsasz is old enough that he might have a hard time keeping up with Batman, but a 45-year-old psychopath with knives can still be plenty terrifying. Anthony Hopkins was even older than that (he was 54) when he played Hannibal Lecter in Silence of the Lambs. Still don't believe me? Then go watch John Lithgow as the Trinity Killer on Dexter. He was 64.
Ian McKellen was 61 when he played Magneto in X-Men (2000), but if Magneto was 10-12 years old during WWII, he should have been more like 70. That's a 9-year difference, which is pretty close to some of the age shifts on Gotham. It's just not as notable, because he was older.