In general, using updated D&D material is recommended over the original material. Wizards of the Coast didn't do this a lot in 3.0/3.5's product lifecycle, but when they did, there was usually a reason for it. (Exception: Things like the Tome of Battle Errata, which is obviously broken.) Personally, I'd not allow the 3.0 version on these grounds alone - the 3.5 version has mechanically overridden it.
But in this case, your primary concern seems to be "balance" rather than it coming from 3.0. Whether the feat is "balanced" for your game is going to depend heavily on your definition of the term. See this question on what makes something overpowered. Using @mxyzplk's definitions, I'd say this feat is trivially overpowered (compare: Spell Focus), but I doubt it is contextually overpowered (it does not provide unusual power in one specific context, the bonuses are highly generic) or even practically overpowered (an extra spell and/or +1 to save DCs isn't going to make a non-dominating character suddenly dominate). Using @Brian Ballsun-Stanton's definition, I'd call it somewhere between balanced (it's certainly useful for most, but hardly mandatory) and underpowered (if your casters are rocking out on metamagic feat chains, taking Spellcasting Prodigy is just a speed bump on the road to power) in a 3E + PF game, depending on the optimization level of your group.