I think there are some pretty important variables that we forget too:
1. Sure, Metal Gear Solid 3D is the only Metal Gear game to release on a Nintendo console since Brawl, but it came out only a month before Kid Icarus: Uprising, which means it was still very new when development began on Smash Bros. If the character roster really has been around since the beginning of development, "relevance to Nintendo" would not have been an issue with Snake's inclusion due to him starring in a heavily promoted 3DS title that was only a month old at the time. The game is still only just over two years old, so Metal Gear has actually appeared more recently on a Nintendo console than a lot of Nintendo series with Smash characters. Certainly more recently than Mega Man.
2. Snake was not included in PSASBR, despite being a pretty obvious choice. Raiden was included instead. At the time, many people thought the reasoning was obvious: Snake belongs to Smash Bros, a rival game. What has really changed since then other than our optimism?
3. We now have both Kojima and a Nintendo rep giving non-answers when asked directly if he's in the game. Why not just rip the band-aid off? It's also worth noting that if Snake is in the game, there is no way that Kojima doesn't know. His insistence that he has no idea either way is pretty transparently bs. He would have to be approached in order for them to use the character.
4. Konami has been pushing Metal Gear pretty hard these last couple years, almost to the exclusion of all of their other series. From a business perspective, how is it logical to exclude the face of the series from what is sure to be one of the biggest game releases of this generation? I'm living proof that Brawl introduced more people to Metal Gear, so why would Smash 4 be any different? We're essentially in the same position we were with Brawl and MGS4: a numbered entry in the Metal Gear series is coming out soon, exclusively for non-Nintendo consoles, and is supposedly a darker and more adult take on the series. Snake made it in then, and he could make it in now.
Here's my new policy. So long as there are other unannounced starter veterans who are obviously returning, Snake's announcement is possibly being saved for a later date. If we get reveals of Wario, Meta Knight, and Ice Climbers, and there's still no sign of Snake, then and only then should we give up hope. At the moment, it's clear that we're not finished with character reveals until release. Snake could be one of them. There is certainly going to be a Direct between now and release, and there's no reason to believe that a new character announcement won't come like it has with every single general direct since the game's announcement at last E3. This was the same way Sonic was revealed, and Snake being saved for last makes sense, especially since it becomes a more surprising and exciting reveal every second that they keep us waiting.