There is sometimes variation where a person needs to learn which each number for which thing uses which system. For example, with people, a common way of counting is "hitori", "futari" (your irregular cases), and then "san nin", "yo nin", ... (your regular cases). It's not always that way; but the flexibility exists and that is quite different from Chinese.

The sound change -hon to -ppon and similar sound changes are not actually regular in Japanese -- there's not a clear phonological rule for them. Although counters don't generally vary in pronunciation for each count of the counter, many of the common ones do; and these variations must be learned per number, per counter.

The earlier commenter spoke to characteristics of Japanese that might seem unique to a student. Counters certainly are shared with Chinese; but these other things -- the variation in the numbers and the variation in the counter, itself -- are not.