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Sherlock supposed he had a less than perfect understanding of the concept of beauty—his sense of aesthetics did not mesh well with others, he'd noted—but he was quite sure about this:
John was beautiful.
Not particularly handsome, nor pretty. Oh, John wasn't the least bit pretty, Sherlock realised that: he was a sociopath, not an idiot.
He also realised, albeit in hindsight, that blurting such a thing out loud, apropos of nothing, in public, was behaviour perhaps outside the culturally acceptable norm. Such were the pitfalls of sociopathy. John had, with characteristic John-ness, looked confused and embarrassed, and had tried to laugh it off as a joke. Seeing his discomfort, Sherlock refrained from elaborating further.
Nonetheless, it was true. For if beauty truly was in the eye of the beholder, then Sherlock was uniquely qualified to make the assessment. He beheld John: not with that shoddy, cursory sort of regard that passed for beholding among the vast majority of the populace (the poor sods); but with focussed observation and keen attentiveness to detail. He beheld John at every opportunity and under every condition, with unwavering interest and a single-minded intensity that others would have mistaken for obsession.
Sociopathy did occasionally have its advantages.
What Sherlock beheld was a man of courage, of honour, of compassion. Scarred, admittedly, but the scars did not detract from John's beauty. Not even the emotional scars, which had the potential to be far more disfiguring than the physical ones. No, here was a man, a soldier, who had come through the fire of battle, not unscathed, but tempered and honed because of it.
He was loyal, John was, in a way that Sherlock was only beginning to apprehend. They had barely met when that loyalty was put to the test. John knew so little about his brand-new flatmate—far less than Sherlock had already deduced about him, naturally—but that had not stopped him from leaping, gun in hand, straight into the fray. On the contrary, despite any private misgivings he might have had, John had deliberately allied himself with Sherlock against the police, against Mycroft, against... well, against the world.
If Sherlock had been a romantic, fanciful sort, he might even have called John a kindred spirit, the other half of his soul... but of course, he was not any such thing.
What he was was a man of science, of logical thinking, of critical analyses. A man of intellect. John did not always follow his mental leaps, but then again, there weren't many who could. In any case, that wasn't the issue. John might not know Sherlock's thoughts, but he did know Sherlock.
There weren't many who could do that, either. In truth, Sherlock hadn't thought there was anyone, until now.
The conclusion, then, the end result of his beholding? Really, his scrutiny was so thorough that it left no room for doubt whatsoever: John was beautiful.
John would simply have to reconcile himself to that fact. Sherlock made a mental note to find a more socially appropriate moment to tell him so.