Well firstly I don't agree with you. Some names with an a at the end are nice and some aren't, just as with many other names.
Of the names you list I don't think there is much to choose between some of them (Louisa/Louise sound very similar to me) some of them are lovely both with an "a" or without (Helen/Helena and Ann/Anna, although I prefer the look of Anne to Ann) I like Susannah much more than Suzanne, and Dorothy more than Dorothea.
I don't think that the "a" makes them sound girly or feminine ("ie" is a much softer sound than "a"). They are all strong names IMO, and if you like them, then pick one.
Names do go in and out of fashion, there is a strong cyclical trend and people are influenced by all many things, from favourite grannies (the general cyclical pattern) to film stars, to avoiding the names of people you went to school with. Sometimes knowingly and sometimes less so.
Some "a"s are about turning a boys name into a girls name, but plenty aren't, and there are quite a few female diminutives: -etta/-ette, -ina/-ine, -ella/-illa as well as -a. I think that the "a" variant endings are Latinate and the "e" French.