The project is among a 45-point plan for major upgrades to Scotland’s transport system over the next 20 years announced on Thursday.
It accompanies schemes named in an earlier stage of the strategic transport projects review (STPR) last year, such as a “mass transit” system in Edinburgh that could include new tram lines, and a “Clyde metro” in Glasgow, which may involve “bus rapid transit” and trams.
The STPR2 report, which will go out for consultation until April 12, also includes a bus-based “rapid transit” system for Aberdeen, connecting the outskirts with the city centre such as via the A96, A944 and A956.
In south west Scotland, improvements to the A75 and A77 to the Cairnryan ferry ports are also recommended, which could include “enhancing overtaking opportunities, widening or realigning carriageways and improving junctions”.
Stranraer station, which remains on a harbour pier a decade after Northern Ireland ferries were switched to Cairnryan, could be upgraded or relocated.
While many of the schemes are at the proposal stage with only outline details, some are confirmed projects, such as bypassing the landslide-prone A83 Rest and Be Thankful pass in Argyll.
The report said the new fixed links to and within the Hebrides would improve reliability and speed up journeys.
It recommended “further work is undertaken on business cases to better understand the benefits, costs and challenges associated with these options”.
"These studies would consider the feasibility of replacing existing ferry services currently delivered by CalMac," the report said.
They would also “ascertain the potential savings associated with the public sector subsidies required to operate the ferry services, and involve input from communities that may potentially be affected”.
However, the proposal looks likely to run into opposition in Mull.
Joe Reade, chair of the Mull and Iona Ferry Committee, said: "We surveyed islanders on this in 2019 on this topic and the response was overwhelmingly negative, so it would seem people value their island identity.
"What they want is a reliable ferry service, dependable in typical winter weather and has space for everyone who wants to use it in the summer.
"Rather than distracting us with grandiose plans for 20 years hence, what is really needed is a two to five year plan to fix the chronically dysfunctional and expensive ferry system."
Colin Howden , director of sustainable transport campaigners Transform Scotland, was also sceptical.
He said: “I doubt any of these suggested crossings will ever be built.
"They look as improbable as Boris Johnson’s failed Irish Sea bridge proposal.
“The Barra and Harris bridges alone would cost billions to build.
"With only 27,000 inhabitants in the Western Isles, the benefit-cost ratio for these proposals would be extremely poor.
"The focus should be on sorting out failing ferry services rather than promoting fanciful road bridges.
“Of course, any bridge to Mull would have to be a joint road-rail bridge.
"It would surely be inconceivable nowadays to be building a new bridge only to carry cars.
"As such, I look forward to my invitation to the first direct Edinburgh to Tobermory rail service under the new ScotRail franchise.”
There is little new detail on the Edinburgh plans beyond those in the initial STPR2 report.
The new document said: “The system would focus on key corridors of demand as well as where congestion impacts on bus services and where public transport is more limited, including targeting more disadvantaged areas where there can be greater dependence on public transport.”
It recommended Transport Scotland “works with regional partners to develop and enhance the cross-boundary public transport system for the Edinburgh and south east Scotland region, potentially comprising tram and bus-based transit modes including bus rapid transit”.
"This would complement and integrate with the region’s current bus, tram and rail networks, to provide improved connectivity between Edinburgh and the surrounding communities, as well as more direct connections between communities outside Edinburgh.”
Transport secretary Michael Matheson said: “The STPR2 recommendations support the measures set out last week in our route map to reduce car kilometres by 20 per cent by 2030 and represent a major piece of work by this Government to make Scotland – all of Scotland – more sustainable.
“This review represents a repositioning of our transport investment priorities. The focus is firmly on how transport can help us protect our climate and improve lives.”
Glasgow City Council leader Susan Aitken said: “Clyde Metro will be transformational, reducing social and economic inequalities, delivering on economic growth, better connecting outlying and poorly served communities and incentivising large-scale modal shift from private car to public transport.”
A spokesman for AGS Airports, which owns Glasgow Airport, said the project “will have a transformative effect in reducing carbon emissions, boosting public transport and alleviating congestion on the M8, one of Scotland’s busiest sections of road.
“The Metro system will not only connect the city to its airport, it will also serve the neighbouring innovation district and business parks opening up more jobs to people across Greater Glasgow and the west of Scotland.”
Dr Martin Bartos, chair of Strathclyde Partnership for Transport (SPT), which runs the Glasgow Subway, said: “SPT looks forward to working with Transport Scotland and Glasgow City Council on the details of this scheme which has the potential to transform the public transport network across the Clyde Valley.”
Karen McGregor, director of capital programmes for cycle path developers Sustrans Scotland, said: “We welcome the recognition of the strategic role that walking, wheeling and cycling can play in achieving the Scottish Government’s objectives.
"This helps to demonstrate the step change in thinking that is needed to meaningfully tackle climate change, improve Scotland’s health and well being, reduce inequalities and deliver sustainable economic growth.”