Having it as an interstate doesn't harm anything at all. Yes it was money that could have been used for something else, but in the long run it does mean that Wisconsin is now stuck with keeping it an interstate grade road, that cannot be downgraded easily. The only reason we're having this problem is that we are all nerds who feel that it breaks the rules. Rule breaking is allowed as long as the ref lets it slide. The original interstate numbering system was a bit rigid, and back then having two major route numbers in a long distance system would be confusing. But now it isn't as bad. Interstate 41 does imply to a traveler that "hey...this road will be 65-70 mph to green bay and appleton" versus US41 that can imply "it is going to be a 45-55 mph road, two lane, and i am going to be stuck behind a truck in a no passing zone" US41 in Indiana. 60 mph road, except through towns, and when IN63 splits off with the thru traffic it turns into a two lane back road.
One could argue, why isn't I43 between I-90/39 and 94 a 3DI, I-339 or I-894. Why isn't I-57 I-55E. Stuff like that. the rules change, we have to live with them. E/W and N/S splits are technically no longer allowed, so we have to put up with odd numbering that would have been fixed with that. I-41 is I-43W. I-88 in IL could be I80N if it connected properly to 80 via 294.