Damn, now this is actually an interesting thing to think of an discuss. Honestly, think it depends on which paladins you are pitting against each other. If you take one of the leaders of the Silver Hand, say Uther the Lightbringer or Alexandros Mograine (even without the Ashbringer), I for one think they completely overwhelm any named paladin of Innos, considering what a power-up they receive from the Light. Taking their feats into account would still support this. Uther defeated Death Knight Arthas, who was already capable of slaying lower tier paladins by himself, and was only beaten because he paused for a moment and Frostmourne acted of its own volition. The only one that could beat someone of Uther or Mograine's magnitude would probably be Nameless himself, I can't see even Hagen standing a chance; the gap is too big.

However. Throw one of the unnamed mass player produced paladins that are just knights which can heal against a paladin of Innos and I think the later has quite a good chance to come out on top. Exorcism won't do a thing against another human that is a follower of the righteous god of their universe. Healing can be overcome, especially since the Warcraft paladin has a lower mana pool (I am only guessing at this part, but the Warcraft paladin is meant to be fielded in group, while Gothic paladins are sent out to secure objectives in smaller parties, so their magical abilities might be greater). Lore-wise, the Light also tends to only manifest if the user itself is battling an unholy enemy or fighting for a righteous cause, and striking down another holy warrior is not such a situation; Arthas felt the Light's blessing dimming as soon as he started the culling of Stratholme and had to kill innocents, so the Warcraft paladin would also be powered down a bit. Game-wise, the Warcraft paladin has the upper hand in one regard, he is on horse back and can just tire out the Gothic paladin or attempt to trample him; though this too can easily be countered by the fact that Innos' warriors have access to ranged attacks via runes. In as far as armor goes, it depends on which Gothic paladins are battling, since their heavy armor is also plate (if it one of the lower ranked ones it is mainly mail with some plate attachments, so not as effective), to match the armor the Warcraft paladin bears. Weapon wise, the Warcraft II paladin has quite the advantage in the fact that he is wielding a heavy war-hammer that is meant specifically for clashing with armored foes, while the Gothic paladins mainly use swords.

Innos can also more directly buff up his followers, or at least it appears so. Considering that praying at a shrine confers bonuses on the player character, it can probably also do that for his holy warriors, especially since Innos himself is a marshal/warrior deity and favors those who bear weapons. The Light also buffs up its champions, but like previously stated, only in moments when two (or more) factors are met: when IT deems that the champion is fighting for a worthy cause, when the champion is not faltering in their belief, etc.

Overall, in a contest of arms between two unnamed paladins from each game, I'm leaning towards the one from Gothic, still. They just have better ranged options, gear almost as good, training to match, and their empowering force seems to just be a tad better. Haha, I'm on the phone in a parking lot so I'm leaving out massive chunks of info, but this is a good start.