Is there any supporting evidence for this claim? If I took an AES library and changed the order of some inner loop wouldn't it require extensive statistical analysis to notice the difference? Which means instead of throwing a bunch of compute at decrypting me, along with the masses 10 years from now, you would need to get a specialist to specifically target me and spend considerable time.
IIRC Groestl if you switch the inputs between the P and Q functions you'll introduce fixed points ino Groestl. Or take your example of AES, if you changed AES such that the loop which ran shift rows and increase it to run four times, you'd massively damage diffusion and probably have a trivially breakable block cipher. Modern cryptographic primitives are very carefully built, minor changes can be disastrous.
True, if your threat model is exclusively future untargetted attacks ,your algorithm may be safer,but that is not a commonly accepted threat model I think, even for terrorists or banks.
Unless you knew why it was organized the way it is in the original spec, altering it may weaken it. The DES S-boxes were altered by the NSA and everyone was suspicious, but it turns out they had made things stronger:
* https://en.wikipedia.org/wiki/Differential_cryptanalysis
Turns out the NSA was (at the time) over a decade ahead in crypto knowledge than the public.
As it stands, AES is approved for even TOP SECRET labelled information:
* https://en.wikipedia.org/wiki/NSA_Suite_B_Cryptography#Comme...
As are the various ECDH NIST curves that so many people are anxious about.