The basic Counterspell maneuver (without Improved Counterspell) works, without dice roll, but you have to have the *same* spell to counter it with, or one specific to that spell. Someone wants to try casting an Empowered, Heightened, Silent, etc Fireball, you need Fireball to counter it. You don't need to match the level or metamagic elements.
You can also do it with a Dispel, but that's a lot less certain.
When using the Improved Counterspell feat you can use a broader range of spells to block the spell, but it has to be a spell of the same school and at least one level higher.
At a minimum you need to identify that spell, typically with a Spellcraft check. Since that check DC is tied to the level of the spell being recognized/identified, and because the metamagics affect that effective level, I can't see any reason why the Spellcraft wouldn't give you that as well.
On the down side, when you aren't using the same spell then you do need to count the spell slot increases from Metamagic enhancements and Heighten Spell effects. It gets a lot more expensive.
And the maneuver is expensive in other ways: Your caster has to Ready Action to Counterspell, with the Feat or not, which means that your caster is tied up, effectively out of the conflict while theirs is free to do whatever is needed, outside of casting a spell.
In our games people have kept pushing my various spell caster to become better at melee. Not because they think I'm going to rush to the front line, but because they know my Wiz or Bard, or Sorc or whatever can still "fight defensively" while providing a flank. He/she can Aid Another to improve a companion's effective AC, essentially a Shield Bearer or an "I've got your back" thing. So my primary or secondary spell casters were still able to contribute when low on spells, or when facing a foe that spells didn't work well against. Or when some smarta.. er.. alec tries to get cute with Counterspell. I effectively take him/her out of play by not triggering their Ready Action.
So there's a reason we don't see that maneuver very often. No real need to make it harder.