Various kinds of structured ASICs have been proposed that can customize logic functions using a few photomasks, which decreases the initial cost, especially that of expensive photo-masks. In the past, we have developed a via programmable structured ASIC “VPEX2” (Via Programmable logic device using EXclusive-or array) that is capable of changing logics on 2 via (the 1st and 3rd via) layers. The logic element (LE) of VPEX2 is composed of EXOR gate and 2 NOT gates. However, “VPEX2” architecture has the two important penalty, the area penalty is 5-6 times that of the ASIC and wiring congestion by detouring wires to avoid I/O terminals. In this paper, we propose a new architecture “VPEX3” in order to achieve the practical structures. In VPEX3, we applied three techniques for decrease area penalty and higher wiring efficiency: (1) LE area is reduced approximately 60% by omitting 1 NOT gate on a LE and the gate width reduction, (2) the kinds of configurable logic function on a single LE is increased from 13 to 22 by introducing “flexible AOI gate technique” and (3) flexible I/O terminal by introducing 2nd via as a programmable layers. Furthermore, the delay model for via programmable wiring is necessary in order to evaluate via programmable wiring architecture compared to standard cell ASIC. We extracted wiring delay characteristics from the ring oscillator test circuit using both of normal wiring and via-programmable wiring. These three new architectures and via programmable wiring-delay-model revealed that an area-delay product of “VPEX3” is as small as twice that of ASIC. Chip-cost estimation among FPGA, “VPEX2”, “VPEX3” and ASIC revealed that the “VPEX3” is the most cost-effective architecture for Systems-on-chips (SoCs) whose production volume is from one thousand to several tens of thousands units.