By all rights, the paladin really should be chopping the cleric up into little bits. It might take forever, but every time the cleric heals a wound the paladin made, the paladin makes just another one.
If you want a good, generic example, though, the best one to use would be the generic NPC's from the DM's Guide, and spells and domains from the Core book only. Otherwise, it turns into a smorgasbord of whipping out one book after another, screaming "18 Charisma that! Divine Might this! Owl's Wisdom here! Fortunate Fate there!". Craziness. Every book that gives one advantage to one class, has been countered elsewhere, be it from a feat like Power Critical, or a spell like Fortunate Fate. Even if the DMG NPC's aren't particularly great, they're still about on par, as far as feats and the like go.
I started taking things apart really only for 1st and 5th level. However, it essentially breaks down like this:
Presuming the cleric is not evil, things are fairly even. At first level, the paladin is favored, though barely, if the cleric plays his cards right. After that, things become a bit less clear.
At fifth, for example, if a cleric loaded up on Hold Persons, there's no way that the paladin's going to survive except through sheer luck; three Hold Persons nearly guarantee the paladin is going to f' up a save then join Coup des Grace ville for five rounds, and at that level, the paladin doesn't have enough tricks to swat the cleric down in three rounds. Even if he did, that just means the cleric resorts to heal, Hold Person, heal, Hold Person. However, most clerics likely won't have more than one or two Hold Persons prepared at 5th level, in which case, the paladin, in my opinion, becomes the favored combatant. Though, only barely.
Past that point, although the paladin does have poor Will saves, this is countered by the fact that they should have a decent Wisdom and good Charisma, both of which will put the paladins Will saves on par with the cleric's spell save DC's, at least up until 13th level. Fortitude goes without saying, and cleric's have few Reflex-related spells, to my recollection, and of them, few are the save or be seriously screwed sorts. At ninth, a Flame Strike can be quite detrimental to our erstwhile paladin, but I'm not sure it would be the deciding factor. Still, I think that this point that even a clerics general assortment of spells has enough to deal with the paladin. A Flame Strike, at least one or two Domain spell goodies (a decent number of which are also direct, damaging spells), a bit of healing when the need requires, and buff spells (even if cast during the combat - the cleric has enough healing, at this point, to make up for a lost round or two) should see the cleric through.
As for 13th? Even with 3.5 Harm, I put my money on the cleric. 65 points of damage from a Harm spell (which will likely hit), then a Flame Strike which whip out 40 or so damage, a Heal for the cleric, and a number of other tricks which have built up over the levels, well, I think the paladin would lose out.
But, I could be mistaken.
