Is there research suggesting that VFR cruise altitude rules improve safety?
Searching Scopus for (VFR OR 'Visual Flight Rules') AND safety in title/abstract/keywords yields two publications (out of 99 hits) that might contain information (or references to other sources) on the safety performance of the current VFR system with alternatives.

Prinzel et al. (2011) - Flight deck interval management and delegated separation for equivalent visual operations


  An emerging Next Generation Air Transportation System concept Equivalent Visual Operations (EVO) can be achieved using an electronic means to provide sufficient visibility of the external world and other required flight references on flight deck displays that enable the safety, operational tempos, and visual flight rules (VFR)-like procedures for all weather conditions. Synthetic and enhanced flight vision system technologies are critical enabling technologies to EVO. Current research evaluated concepts for flight deck-based interval management (FIM) operations, integrated with Synthetic Vision and Enhanced Vision flight-deck displays and technologies. One concept involves delegated flight deck-based separation, in which the flight crews were paired with another aircraft and responsible for spacing and maintaining separation from the paired aircraft, termed, "equivalent visual separation." The operation required the flight crews to acquire and maintain an "equivalent visual contact" as well as to conduct manual landings in low-visibility conditions. The paper describes results that evaluated the concept of EVO delegated separation, including an off-nominal scenario in which the lead aircraft was not able to conform to the assigned spacing resulting in a loss of separation.


Quinby (1980) - General aviation operating requirements for the 1980's


  This paper presents a review of the use of the airspace and the air traffic control system. Safety, capacity and efficiency of this use under Visual Flight Rules (VFR) are compared with the evolving constraints imposed by operations under Instrument Flight Rules (IFR). The concept of Electronic Flight Rules (EFR) as developed by Topic Group III on Freedom of Airspace in the FAA’s 1978–79 E &amp; D Initiatives Process is reviewed. The potential for conservation of air traffic control manpower and aircraft fuel is further developed. Promising areas for further technical exploration are noted. The paper concludes with some considerations for co-existence of VFR, IFR, and EFR traffic during a transition period.