If I find a properly adjusted seat uncomfortable from the start, it'll probably remain uncomfortable for me. Maybe it would've been different with a Brooks, but I've never had a Brooks.
It's possible that your riding style is what can be changed. If you're used to a saddle with a lot of padding, you might be sitting too heavily in the saddle, not putting enough weight on your feet (and to lesser extent hands). You can try putting more "spring" in your legs and arms and unweighting your bottom some. Otherwise... I'd say just replace the saddle. Can't you put the saddle from your old bike onto your new one?