You have to ask: what is the leaderboard for? I'd see it as:
1) A bit of fun vanity, or a challenge -- see how high you can go.
2) A way to find reasonable opponents of a similar skill level.
3) A way to measure your own progress.
For all of these, it seems to me that the only way that they work is with a completely level playing field. I applaud the decision to not count games with card restrictions.
If you want to prioritise enjoyment above skill comparison, and for you card restrictions do this, then fine. Carry on restricting, and don't get counted for the leaderboard. Make your choice, either blanket, or for a given game/period.
What this does throw into sharper relief, though, are those people who constantly refuse games on automatch. If you have card restrictions, use them and challenge, or use veto mode. Otherwise you're just trying to have your cake and eat it.
I'd be happy to hear a case I haven't considered for putting automatch on and then refusing games, but until I do, I think I'll be refusing further games myself from anyone who switches on automatch and then refuses a game (it's also kind of annoying when there are few people in the room and you keep getting matched with someone who keeps refusing).
Ps. I don't see Paralyzed there now. Has dougz dealt with it?