Hmm if you look at a map of Manila, the proposed NLEx SLEx Connector Road and the current Skyway Stage 3 aren't too far from each other.There is a separate expressway above the PNR alignment connecting to NLEX. They're building two expressways to connect NLEX and SLEX, FYI.The PNR alignment is too far west of manila to provide needed convenience to the rest of Metro Manila.
In addition, what you want, to respect private property (i.e. not expropriate any property) is impossible for an efficient infrastructure. You say that the alignment along the San Juan River is impractical. What more if less expropriation of private land was made?
JICA actually studied all routes to and fro NLEx and SLEx (thru Araneta, thru PNR) and found that the PNR alignment is far more optimal (less ROW issues, less businesses affected, less curvy alignment, more spaces between buildings and the viaduct, etc) than the Araneta route - with the PNR alignment, there is also an option to build rampways thru Espana - Q Ave and Ramon Magsaysay - Aurora Bvd that could further decongest the roads. The MMS3, for example, doesn't even have a direct exit to Aurora Boulevard/Magsaysay.