I like that ES trades can be out of sync with SPY - that's the whole point, while they do most of the same or similar trades, SPY will catch trades that ES misses and ES will catch trades that SPY misses.  If they both did the same trades I wouldn't bother with the ES signals. If you don't have the other ETF's then you want ES with SPY because you fill in more trade dates that way - get more opportunities, that's the whole reason I even added it. SPY might do a trade for 1 or 2 months at times but ES will generally catch a trade or two during those air pockets when SPY is stubborn. 

with the other ETF's in the mix the ES will probably no longer be needed for that as they would provide the additional trades to catch trade opportunities that SPY would miss. 

SPY and ES are 99% correlated - but they are way different prices and ES trades 23 hrs a day unlike SPY and SPX cash. The systems get their signals from price levels that various indicators are are at, and when you have different prices the RSI is not going to be in the same spot on SPY as it is on ES, same for other indicators, just common sense