Every node validates EVERY input of transaction, it means that 1 input = 1 transactions search. 100 inputs = 100 searches.
Correct, but it only needs to search through the UTXO. (The very limited list of unspent transaction outputs).
The node only needs to do a full blockchain scan once, when building the UTXO list during synchronization. Then it's 100 very fast searches through a short list.
That's 1 search through a list of every transaction in the entire blockchain every time it needs to validate a transaction, just to see if that transaction has ever existed before.
Additionally, it needs to maintain and scan a separate database of every address and the current balance of each address, just to see if there are enough bitcoins available.
Inputs solve both of those problems quickly and efficiently with a single fast search.
While you are thinking about that, how would your system handle the bitcoin scripting system that allows for multi-sig and other useful extensions? Are you suggesting we just abandon that feature?