How to avoid the "you didn't consider this" review in a scientific publication?
I empathise with your difficulty and wish there was an easy fix. However, going by the question and comments, it does seem like you may need to rethink your approach a little. Consider the following:

(1) In an applied research field, the bar is not just solving a sub-problem; it is ensuring that the proposed solution will work with all other factors considered. To give a very trivial and crude (pardon me) example, if a car bonnet has to be light and strong, you cannot treat the two independently and use polythene (solving light) or concrete (solving strong). 

The comment : "There is no way this is going to work when you consider E.c and E.d as well"." seems to suggest exactly that. I know my example is not perfectly analogous to your problem, but I hope the essential message is conveyed.

(2) There exists an industry standard S. Therefore, any proposal to change has merit only if it can replace S on all counts. If the method S scores 70%, 80%, 60% on some relevant metrics, your method E should not score 100%, 10%, 80% , even though 2/3 metrics are significantly improved (because one metric has fallen, and that could be unacceptable). Rather, an incremental 75%, 85%, 65% would be more acceptable.

There is a constant strain in such fields between novelty and applicability,  both need to be balanced out. Depending on what conference it is, one may carry more weight than the other, but the application bit can rarely be ignored.

What seems to me a better approach is:

(1) Tackle Eb/c/d in your study, even if briefly. Not just in the introduction, in the study and the results itself. Show that you are not simply highlighting problems (i.e. mentioning only in introduction), but doing something about them even if you don't solve them fully. Even analysing and rating the magnitude/importance of Eb/c/d is a meaningful contribution, supplementing your main work on Ea. So you don't need to solve them all, but you do need to consider them and look at inter-dependence.

(2) If possible, suggest ways in which E can be integrated with S. Then, the benefits of Ea can be used without the problems Eb, Ec. Again, you don't actually need to integrate the whole method. Look at ways to do it, what problems exist, how meaningful such an exercise is vs replacing an entire system.

These approaches should be good for such conferences which are indeed intended to share a developing idea. Even in those, your eye must be on the future- on how to develop it, what can be taken forward, what can be done to make it more complete.