It's not necessarily bad though. As you said, it changes dynamics. Players just need to adjust, much like adjusting to a straddled pot, or stand up game in cash.
@Defarse In the end, it all comes down to preference. I think tournaments play better when there is more pressure to play hands and win pots because of the ante. No limit hold em traditionally was always played with an ante. It wasn't until online poker came along that the ante was eliminated in NL cash games.
As I noted earlier, less experienced players don't really adjust correctly to the ante. They won't adjust their ranges for it. They won't try to steal more often. But I've played a decent amount with people that understand the dynamics, and playing without an ante in a tourney causes MUCH tighter play.
Hell, I played a tourney they other day where everyone started with 7k and the house did a 10k splash at each table on the first hand. It was a 7 way limped pot at my table. That shouldn't have happened. What's silly about it, is that if I had jammed pre (which I probably could have in theory), I would have gotten called. But the other players wouldn't take that aggressive action themselves. So I took the free flop from the BB with A6s and won a checked down pot with TP.
Point being, people don't adjust. So whether you use an ante in a home game or not is largely irrelevant outside of being consistent with casinos or in the event you have a lot of players that play a decent amount of casino tournaments.
As far as starting stacks, casinos don't start you with more because of the ante. And those run just fine. But if you have extra, using 15 T100 and 4 T500 (instead of the casino tradition of 10 and 2) to start is a good idea. T1k and T5k don't matter as much because by the time they hit the ante, chips will have consolidated a good bit. Using more than 4 T500 per player is just not necessary. It's the most useless chip denomination since it's only half of the next chip.