Carl said he was considered a suspect for 90 days, not after that. Other people may have blamed Carl, but it wasn't the FBI.
You don't know what they were doing for the last 18 years. They can only follow leads that they have, and generally in these sorts of cases if they don't get anything solid in the first week or two the chances of solving the crime becomes very bleak unless they get incredibly lucky. If a body isnt found eventually then those cases usually are never solved.
After that it becomes a management issue, do you dedicate massive resources on an old crime with little chance of success or do you focus those resources on more recent crimes. The answer to that question should be pretty obvious to anyone with an ounce of sense. As time drags on newer crimes which have a better chance of being solved become a higher priority. Jaycee's case would have become cold a very long time ago, with little hope of progress until someone found her body (and, unusually, in this case the body turned out to still be alive - that allmost NEVER happens though). There were probably allways some cold case investigators looking at her kidnapping over the years, but they would be following up new leads as they came in, and as months turned to years, those leads would have trickled down to allmost nothing.