While I don't know a lot about Lithuanian, even though I want to study it in the far future, I want to have a word or two about the IE things. It's true that Proto-Indo-European most likely originally had two genders (animate and inanimate which correspond to later masculine and neuter), however that doesn't mean that a non-existence of a feminine gender means any preservation of something archaic. The feminine gender developed in Indo-European after the split of the Anatolian languages, which was the very first language group to split from PIE, but before the split of other language groups. None of the Anatolian languages survives until today, so all IE languages nowadays are derived from a common language that had three genders. If you study classical IE languages such as Latin, Ancient Greek and Sanskrit, it's rather obvious that masculine and neuter differ somewhat from the feminine gender. When analysing this, you must keep in mind though that there were two different types of declension in these languages. There were declensions that are nowadays believed to be the older declensions, corresponding to the Ancient Greek 3rd declensions, and to all declensions except the o-/a-declensions in Latin, and the "younger" o-/a-declensions in Latin and Greek (only a-declension in Sanskrit, cause short 'o' merged with 'a', if I recall correctly). In these "older" declensions there isn't any difference between the masculine and feminine gender, and the neuter only differs in nominative and accusative singular and nominative and accusative plural.
Compare these Latin examples:
limen (threshold, entrance) - neuter
-----Sg.----- Pl.
Nom. limen limin-a
Gen. limin-is limin-um
Dat. limin-i limin-ibus
Acc. limen limin-a
Abl. limin-e limin-ibus
victor (victor, conqueror) - masculine
-----Sg.----- Pl.
Nom. victor victor-es
Gen. victor-is victor-um
Dat. victor-i victor-ibus
Acc. victor-em victor-es
Abl. victor-e victor-ibus
victrix (female conqueror) - feminine
-----Sg.----- Pl.
Nom. victrix victric-es
Gen. victric-is victric-um
Dat. victric-i victric-ibus
Acc. victric-em victric-es
Abl. victric-e victric-ibus
So it seems to me that there hadn't been any clear distinction between the masculine and the feminine gender at the time that this kind of declension was "invented". Only the later declensions really have a gender assigned to them. The vast majority of words declined according to the o-declension is masculine or neuter, and the vast majority of words declined according to the a-declension is feminine. Yet again the nom./acc. sg./pl. forms are the only ones that differ in masculine and neuter words in the o-declension, showing that these belong together, being nearly the same originally:
servus (slave) - masculine
-----Sg.----- Pl.
Nom. serv-us serv-i
Gen. serv-i serv-orum
Dat. serv-o serv-is
Acc. serv-um serv-os
Abl. serv-o serv-is
frumentum (grain, crops) - neuter
-----Sg.----- Pl.
Nom. frument-um frument-a
Gen. frument-i frument-orum
Dat. frument-o frument-is
Acc. frument-um frument-a
Abl. frument-o frument-is
Compare a word of the a-declension:
serva (female slave) - feminine
-----Sg.----- Pl.
Nom. serv-a serv-ae
Gen. serv-ae serv-arum
Dat. serv-ae serv-is
Acc. serv-am serv-as
Abl. serv-a serv-is
There are several similarities between the feminine a- and the masculine o-declension as well which aren't obvious at once. As I once read that the o- and a-declensions were constructed for derivatives originally, I tend to think that o- and a-declension originally were the same with only a different thematic vowel (a instead of o). If you take into account that long "i" which occurs twice in the masculine o-declension is derived from an "oi"-diphthong and "ae" resembles an "ai"-diphthong (further support for this in Ancient Greek), you get a lot of similarities, but I don't think I should elaborate further on this, as this is a forum for Lithuanian
I don't know anything about different declension classes in Lithuanian, it would be cool to compare it to this. However, Lithuanian having three genders is more archaic in that respect than Latvian having only two genders, because PIE had two genders in the very beginning only, long before something called "Baltic" nowadays began to arise. (You might say, Latvian having two genders like earliest PIE is a 'secondary' development)
Oh and by the way, the third person singular and plural differed in PIE verbs, but there were two different ways of conjugation, and I couldn't elaborate on that as much anyway.