If you like both names equally but don't have a particular reason for choosing Margaret eg. it's not a family name or that you really adore one of the nn's (Greta, Peggy, Meg, Margot, Maisie, Maggie, Mae etc), I'd stick with Elizabeth as it's far more timeless.
As far as I'm aware Elizabeth is the only girls name that has stayed in in the E and W top 100 every year since records began in the 1300's. An Elizabeth could be easily be any age and any social class - yet thanks to it's dozens of nn choices and the fact it hasn't been in the top10/20 for a while, the name doesn't feel overused imo.
Where as most Margaret's are more likely to be 60 plus - although there will be some younger girls with the more popular diminutives/variations around (Margot is currently trendy for example).