I say we can take into account more subjective things like how fun it makes UU. Come on now, we aren't all complete idiots, and some of us are capable of making judgments.
First, the argument of "allow all NFEs or allow none" doesn't work. We don't "have" to do anything just because we did it in a completely different scenario. We're allowed to allow Pikachu because it has Light Ball but ban Grovyle because it's the same as Sceptile. We can allow Vigoroth in UU because it's not too strong but ban Chansey if we feel it's too strong.
However, my stance is that we only allow distinct Pokemon. A distinct Pokemon is a Pokemon that functions better in some way than its fully evolved counterpart. This means we do not, for example, have to allow Surskit because it has a different typing than Masquerain, because Masquerain's stats more than make up for any weaknesses and lack of STAB.
The list of NFEs that I would consider "distinct" is: Pikachu, Clamperl, Vigoroth, Trapinch, Scyther, and possibly the NFEs that have a Speed advantage, such as Onix, Electabuzz, and Magmar. Porygon2 is also a good idea for inclusion, as Trace can be a unique trait, and Porygon2 can tank, something PorygonZ cannot do. Pupitar's trait (or more accurately, lack of Sand Stream) make it play somewhat differently as far as team relations go, and STAB on Earthquake means it's actually stronger than Tyranitar's EQ. I think Pupitar is still the only DD + STAB EQ Pokemon (and thus has the strongest DD EQ).
To whomever mentioned Shelgon using Double-Edge to sweep, consider that STAB Dragon Claw has the same power as Double-Edge, hits Dragons harder than Double-Edge thanks to being SE, hits Rocks harder thanks to not being resisted, hits Ghosts harder thanks to actually hitting them, and hits Steels just as hard because both are resisted. Everything else is neutral to both, and thus is hit just as hard by both, meaning Shelgon won't use Double-Edge on anything.
To quote myself from the last topic,
To me, the entire purpose of UU is to have a metagame different from OU. Allowing NFEs of OUs in UU defeats that purpose. Almost every NFE is played exactly like its fully evolved counterpart, except there are usually even less viable strategies with them (Shelgon can't really run a devastating special set, for instance, but Salamence can). This is what is meant by "OU-lite". Saying "they won't be used" is not a valid argument. If they aren't used, it doesn't matter if they are banned from OU, so there's really no point in creating opposition to it by introducing this change. If they are used, they need to be taken into account.
Pokemon should be played, in the "major" tiers (so not stuff like Little Cup I guess), with "distinct" Pokemon. What this means is that it is either fully evolved, or has something unique to set it apart from its fully evolved counterpart.
Pikachu has Light Ball to make its offensive stats much higher than Raichu's.
Trapinch has Arena Trap to give it a purpose over Flygon.
Vigoroth lacks Truant, meaning it doesn't have to be a hit-and-run Pokemon, but can actually set up, or just hit stuff on consecutive turns.
Clamperl can use DeapSeaTooth and DeapSeaScale (although the Defensive boost is overshadowed by the pathetic HP, the increase to Special Attack makes it a potential offensive powerhouse).
Scyther has signficantly more Speed and a separate typing from Scizor, granting it immunity to Ground, 4x resist to Fighting, and STAB Flying.
Pupitar's Earthquake is actually more powerful than Tyranitar's, and Sand Stream can be a double-edged sword. Duskull gets Levitate over Dusknoir and Dusclops. Onix has signficantly more Speed than Steelix, trades a few weaknesses / resistances, and has STAB Rock.
I cannot think of any Pokemon that aren't watered-down versions of their fully evolved counterparts, and I see no reason for the others to be allowed in UU.
I am of the opinion that, except for the preceding list, all NFEs should be in the same tier as their fully evolved counterpart.
To expand on my opening part about Salamence vs. Shelgon...
Almost every NFE is played exactly like its fully evolved counterpart, except there are usually even less viable strategies with them: Shelgon can't really run a devastating special set, for instance, but Salamence can. Both can use a physical set, though, so what you have is something that's essentially a watered down version of it. Salamence's higher HP and Special Defense more than makes up for its increased weakness to Ice and Rock, as well as the lack of resistance to Electric. Intimidate and more HP means it takes less from physical attacks, despite the slightly lower Defense. It only takes slightly more from Rock moves thanks to the weakness after you factor in Intimidate.
I disagree with the idea of a "grandfather clause" for Pokemon. This is a new game. What happened in the last gen is completely irrelevant. Just like it brought Forretress up to potential OU rather than BL status, and bumped Celebi, Zapdos, and Snorlax down from OU to BL, we shouldn't see how Pokemon were in UU last gen to see how they are this gen. I don't see anyone arguing about Golbat being in UU, anyway, which seems kind of hypocritical. Crobat didn't exist in RBY, and Golbat was definitely UU there...
If we look at the Pokemon without bias from previous generations, however (which is how I feel we ought to do it), we'll see that there isn't a single thing Gligar can do that Gliscor can't. There is no reason to use Togetic when Togekiss exists, so I don't see why they should be given special treatment.
All non-distinct NFEs should be in the same tier as their fully evolved counterpart. We are allowed to actually use our judgment to decide where to cut things off; we do not have to accept to the slippery slope fallacy of "If we allow Scyther, we have to allow all NFEs in UU" that some people appear to suggest.