I will address your initial question:
- ... are there any major defects in a human that you would expect not to exist if someone (or something) sat down to create the perfect humanoid?
But let's formulate it in a bit different way:
- Would we expect to be able to distinguish between designed and evolved life forms?
Yes, but not necessarily.
A thing which may distinguish designed lifeform from evolved life form is that the first one is bound by the realm of physics, chemistry and other processes affecting or theories describing ontogenesis of the life form.
Naturally evolved life form is not only bound to all mentioned above, but also by inheritance of previous life forms and their particular restrictions and environmental factors which did shape them(their ancestors) in the evolution process before it split to another branch which is a root for the life from we may investigate.
In that regard evolved life form is more constrained in choosing or refurbishing its inheritance and has history, the history behind each element of its existence.
The designed life form is more free in that regard, creators more free to implement different solutions as they are not bound by the necessity of one solution to transit in another solution they may choose solutions from all possible solutions and not care if such thing could evolve naturally, are there some problems in that evolving, is there problem in transiting from one state to another. In that regard flame throwing dragons most likely to be engineered solution. There are tricks to implement, creative solutions to create a system in the way and fashion evolutions won't work.
To ignite a flame - is it possible to use electricity, sure, piezo elements, sure it possible. will it emerge naturally? Not likely - each change in natural selection should be useful or neutral, or at least not that bad. But better are those which get something for the change.
It may be more difficult to detect the creation if creators are copycats. The life from they created may look natural, as it has pieces of the puzzle which may have recognizable historical meaning.
But also we should then take look at the whole ecosystem they exist in. The first question would be to ask if they are part of it and its historical evolution records.
Then to see if their historical records belong to certain branch or multiple branches. Analyzing that data we can essentially tell if they are the probable result of the evolution of the ecosystem. Less probability, with a good understanding of the whole system and processes, higher are chances of their artificial creation.
As for specifics of improvements, it is a broad question and is opinion based part of it. Not all improvements are good in all environments, and they come with the cost of losing some options, because of fundamental limitations of blocks which are used.
As an example - fur is good for the cold environment, but excessive one is limiting mobility in a hot climate. There are incompatible solutions, and more adaptations we may willing to have, higher chances to hit the wall of those incompatibilities.
We may expect a wider spectrum of parameters of environment they can live in - but it is not granted.
And intelligent design may find different solutions around incompatible adaptations and each such trick decreases the probability to evolve naturally, so in a statistical sense, they can be well above average in the system, so we could suspect they are designed or it was a result of a unique situation. Taking into the account other data, we can say more precisely.
Things can be simple as everyone has blue eye's and 10-100 variations of the genes encoding that, depends how long in the past was the last correction.
very thing connection of certain aspects, as an example - not the blue eye, then died in a week or even born dead - it can be a sign of highly packed code, it can be a sign of design. Because naturally evolved life is more acceptable to mutations, more wiggle room for that, as it is a driving force for changes in their development and they are used to that.
So very high mortality rate among mutants and very rare mutations can be a sign. They may look as a diverse system, but it may be static in the diversity and may have a higher mortality rate in newborns than usually average in the ecosystem system.
So there are ways to detect tampering or creation. They aren't guaranteed.
Hardest would be a good creation of a whole system from scratch trying to mask the fact of creation. A system probably can be created to be indistinguishable from a naturally evolved system.
But we can test and try to determine how is the probability of the system to evolve naturally - there can be a difference in probabilities on the average in the galaxy, but we would not be able to catch the hand, just have a probability as a result.
as for improvement - add them more intelligence, the thing is not that much required for survivial, so hard to get too much of it in a natural way ...