I used to have regrets about both my kids names - daughter is Anna, which we chose partly because my husband is German and I am British and it works in both countries - she was born in the UK where it is neither a "common" nor an "off the wall" name, and we knew no other baby or small child Annas... Then we moved to Bavaria when she was 19 months old and it seems like every second little girl is called Anna, including our next door neighbour's daughter who is the same age, and another Anna who is a year older about 10 doors down the road!
My son's name goes the other way - we still wanted a simple name that works in both countries, and found boys names really, really hard (I am a sometime school teacher too, which seems to have strongly put me off some previously perfectly acceptable names, more so with boys names - as well as not wanting to give my son the same name as any ex-boyfriends or family members.). We finally settled on Erik, despite the fact a few people expressed the fact they didn't like it openly we felt right about it - he has Thomas (DH's name) as a middle name, which we thought he could switch to if he really hated Erik).
When DS was under about 2 I had huge doubts about his name some days and really wondered if we should just have named him after DH, even though there are loads of Thomas' here, as at least it is inoffensive... BUT now he is 3.5 he so suits and loves his name (he is a tall, broad shouldered, strong, and stompy 3 year old and the name seems so right) and it is totally his own! He even says he wants us to give baby number 3, due in April the same name as him, so they can both be Eriks!
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I would say give it time - I think Isaac is a lovely timeless name suited to any profession etc. when he grows up, and is not common without being a fashion or deliberately quirky name, and is the kind of name lots of people aim for! You will most probably find your son grows into his name and you cannot imagine him being anyone else by the time he is 2 or 3!